Ben Bolstad
| Snapshot Date: 2025-12-01 13:45 -0500 (Mon, 01 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_22 |
| git_last_commit: d2ce144 |
| git_last_commit_date: 2025-10-29 09:58:55 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-04 12:00 -0500 (Thu, 04 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4878 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4624 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 257/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.74.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.74.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BufferedMatrix_1.74.0.tar.gz |
| StartedAt: 2025-12-01 22:04:43 -0500 (Mon, 01 Dec 2025) |
| EndedAt: 2025-12-01 22:05:07 -0500 (Mon, 01 Dec 2025) |
| EllapsedTime: 24.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BufferedMatrix_1.74.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.74.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BufferedMatrix’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup?
209 | $x^{power}$ elementwise of the matrix
| ^
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘Rcodetesting.R’
Running ‘c_code_level_tests.R’
Running ‘objectTesting.R’
Running ‘rawCalltesting.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.74.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function ‘dbm_ReadOnlyMode’:
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: ‘sort_double’ defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init_package.c -o init_package.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘rowSums’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colSums’ in package ‘BufferedMatrix’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘BufferedMatrix’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘BufferedMatrix’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix", "BufferedMatrix", .libPaths());.C("dbm_c_tester",integer(1))
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
Adding Additional Column
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000
Reassigning values
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 3
Buffer Cols: 3
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Activating Row Buffer
In row mode: 1
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Squaring Last Column
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
5.000000 10.000000 15.000000 20.000000 25.000000 900.000000
Square rooting Last Row, then turing off Row Buffer
In row mode: 0
Checking on value that should be not be in column buffer2.236068
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
2.236068 3.162278 3.872983 4.472136 5.000000 30.000000
Single Indexing. Assign each value its square
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Resizing Buffers Smaller
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Activating Row Mode.
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
Activating ReadOnly Mode.
The results of assignment is: 0
Printing matrix reversed.
900.000000 625.000000 400.000000 225.000000 100.000000 25.000000
841.000000 576.000000 361.000000 196.000000 81.000000 16.000000
784.000000 529.000000 324.000000 169.000000 64.000000 9.000000
729.000000 484.000000 289.000000 144.000000 49.000000 -30.000000
676.000000 441.000000 256.000000 121.000000 -20.000000 -10.000000
[[1]]
[1] 0
>
> proc.time()
user system elapsed
0.246 0.047 0.284
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 478284 25.6 1046725 56 639600 34.2
Vcells 884773 6.8 8388608 64 2081613 15.9
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Mon Dec 1 22:04:58 2025"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Mon Dec 1 22:04:58 2025"
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
>
>
> RowMode(tmp2)
<pointer: 0x563928391370>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Mon Dec 1 22:04:58 2025"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Mon Dec 1 22:04:58 2025"
>
> ColMode(tmp2)
<pointer: 0x563928391370>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.56208800 0.19173021 -1.0210309 0.22856890
[2,] -2.22371348 0.06333479 0.3203122 -0.03601754
[3,] -0.09619041 -0.82570525 -0.2554332 -1.51807163
[4,] 1.23477706 0.48271881 0.6223589 -0.64967798
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.56208800 0.19173021 1.0210309 0.22856890
[2,] 2.22371348 0.06333479 0.3203122 0.03601754
[3,] 0.09619041 0.82570525 0.2554332 1.51807163
[4,] 1.23477706 0.48271881 0.6223589 0.64967798
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 9.9780804 0.4378701 1.0104607 0.4780888
[2,] 1.4912121 0.2516641 0.5659613 0.1897829
[3,] 0.3101458 0.9086832 0.5054040 1.2321005
[4,] 1.1112052 0.6947797 0.7888972 0.8060260
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 224.34289 29.57043 36.12564 30.00946
[2,] 42.13583 27.57998 30.97992 26.93385
[3,] 28.19765 34.91254 30.30947 38.83908
[4,] 37.34683 32.43052 33.51133 33.70994
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x56392938d9b0>
> exp(tmp5)
<pointer: 0x56392938d9b0>
> log(tmp5,2)
<pointer: 0x56392938d9b0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 466.9403
> Min(tmp5)
[1] 53.42225
> mean(tmp5)
[1] 72.6787
> Sum(tmp5)
[1] 14535.74
> Var(tmp5)
[1] 866.067
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 91.93272 67.19050 71.70408 71.11149 72.67111 67.30663 71.68989 71.87894
[9] 68.15833 73.14335
> rowSums(tmp5)
[1] 1838.654 1343.810 1434.082 1422.230 1453.422 1346.133 1433.798 1437.579
[9] 1363.167 1462.867
> rowVars(tmp5)
[1] 7840.86733 94.90580 74.25497 52.83077 102.06110 64.98614
[7] 75.90291 80.66120 71.72793 133.37783
> rowSd(tmp5)
[1] 88.548672 9.741961 8.617132 7.268478 10.102529 8.061398 8.712227
[8] 8.981158 8.469234 11.548932
> rowMax(tmp5)
[1] 466.94034 87.70022 85.86089 86.62420 90.32120 85.47230 92.19530
[8] 91.41037 84.24387 97.25526
> rowMin(tmp5)
[1] 61.54698 53.86364 53.62314 58.78933 53.43713 55.66040 56.20680 54.72003
[9] 53.42225 53.96832
>
> colMeans(tmp5)
[1] 112.48485 67.91996 70.21375 67.61173 71.74676 73.09994 72.45191
[8] 68.63108 69.45795 77.12795 68.16976 69.75234 71.94869 69.52211
[15] 74.32836 71.72906 71.83401 71.63546 66.45595 67.45247
> colSums(tmp5)
[1] 1124.8485 679.1996 702.1375 676.1173 717.4676 730.9994 724.5191
[8] 686.3108 694.5795 771.2795 681.6976 697.5234 719.4869 695.2211
[15] 743.2836 717.2906 718.3401 716.3546 664.5595 674.5247
> colVars(tmp5)
[1] 15590.15976 60.46782 40.05539 105.78793 106.17705 170.04042
[7] 54.35467 63.05105 86.11577 72.26171 107.79203 33.50085
[13] 104.25085 72.84953 94.28507 50.96460 93.91933 68.56359
[19] 142.96441 35.00180
> colSd(tmp5)
[1] 124.860561 7.776106 6.328933 10.285326 10.304225 13.039955
[7] 7.372562 7.940469 9.279858 8.500689 10.382294 5.787992
[13] 10.210331 8.535194 9.710050 7.138949 9.691199 8.280314
[19] 11.956773 5.916232
> colMax(tmp5)
[1] 466.94034 79.21696 85.16910 84.70787 97.25526 92.19530 84.81885
[8] 78.61658 82.37102 85.86089 83.97268 83.03620 91.41037 84.32645
[15] 89.95476 85.47230 86.62420 81.21513 86.37017 79.48383
> colMin(tmp5)
[1] 58.68971 57.16405 63.08520 56.05927 59.35169 54.72003 61.84723 56.66585
[9] 55.66040 61.85775 53.43713 62.37999 58.78933 53.86364 58.04232 63.10707
[17] 53.96832 59.61798 53.42225 59.61687
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 91.93272 67.19050 71.70408 71.11149 72.67111 67.30663 71.68989 NA
[9] 68.15833 73.14335
> rowSums(tmp5)
[1] 1838.654 1343.810 1434.082 1422.230 1453.422 1346.133 1433.798 NA
[9] 1363.167 1462.867
> rowVars(tmp5)
[1] 7840.86733 94.90580 74.25497 52.83077 102.06110 64.98614
[7] 75.90291 83.94743 71.72793 133.37783
> rowSd(tmp5)
[1] 88.548672 9.741961 8.617132 7.268478 10.102529 8.061398 8.712227
[8] 9.162283 8.469234 11.548932
> rowMax(tmp5)
[1] 466.94034 87.70022 85.86089 86.62420 90.32120 85.47230 92.19530
[8] NA 84.24387 97.25526
> rowMin(tmp5)
[1] 61.54698 53.86364 53.62314 58.78933 53.43713 55.66040 56.20680 NA
[9] 53.42225 53.96832
>
> colMeans(tmp5)
[1] 112.48485 67.91996 70.21375 67.61173 71.74676 73.09994 72.45191
[8] 68.63108 69.45795 77.12795 68.16976 69.75234 71.94869 69.52211
[15] 74.32836 71.72906 71.83401 NA 66.45595 67.45247
> colSums(tmp5)
[1] 1124.8485 679.1996 702.1375 676.1173 717.4676 730.9994 724.5191
[8] 686.3108 694.5795 771.2795 681.6976 697.5234 719.4869 695.2211
[15] 743.2836 717.2906 718.3401 NA 664.5595 674.5247
> colVars(tmp5)
[1] 15590.15976 60.46782 40.05539 105.78793 106.17705 170.04042
[7] 54.35467 63.05105 86.11577 72.26171 107.79203 33.50085
[13] 104.25085 72.84953 94.28507 50.96460 93.91933 NA
[19] 142.96441 35.00180
> colSd(tmp5)
[1] 124.860561 7.776106 6.328933 10.285326 10.304225 13.039955
[7] 7.372562 7.940469 9.279858 8.500689 10.382294 5.787992
[13] 10.210331 8.535194 9.710050 7.138949 9.691199 NA
[19] 11.956773 5.916232
> colMax(tmp5)
[1] 466.94034 79.21696 85.16910 84.70787 97.25526 92.19530 84.81885
[8] 78.61658 82.37102 85.86089 83.97268 83.03620 91.41037 84.32645
[15] 89.95476 85.47230 86.62420 NA 86.37017 79.48383
> colMin(tmp5)
[1] 58.68971 57.16405 63.08520 56.05927 59.35169 54.72003 61.84723 56.66585
[9] 55.66040 61.85775 53.43713 62.37999 58.78933 53.86364 58.04232 63.10707
[17] 53.96832 NA 53.42225 59.61687
>
> Max(tmp5,na.rm=TRUE)
[1] 466.9403
> Min(tmp5,na.rm=TRUE)
[1] 53.42225
> mean(tmp5,na.rm=TRUE)
[1] 72.66001
> Sum(tmp5,na.rm=TRUE)
[1] 14459.34
> Var(tmp5,na.rm=TRUE)
[1] 870.3709
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.93272 67.19050 71.70408 71.11149 72.67111 67.30663 71.68989 71.64103
[9] 68.15833 73.14335
> rowSums(tmp5,na.rm=TRUE)
[1] 1838.654 1343.810 1434.082 1422.230 1453.422 1346.133 1433.798 1361.180
[9] 1363.167 1462.867
> rowVars(tmp5,na.rm=TRUE)
[1] 7840.86733 94.90580 74.25497 52.83077 102.06110 64.98614
[7] 75.90291 83.94743 71.72793 133.37783
> rowSd(tmp5,na.rm=TRUE)
[1] 88.548672 9.741961 8.617132 7.268478 10.102529 8.061398 8.712227
[8] 9.162283 8.469234 11.548932
> rowMax(tmp5,na.rm=TRUE)
[1] 466.94034 87.70022 85.86089 86.62420 90.32120 85.47230 92.19530
[8] 91.41037 84.24387 97.25526
> rowMin(tmp5,na.rm=TRUE)
[1] 61.54698 53.86364 53.62314 58.78933 53.43713 55.66040 56.20680 54.72003
[9] 53.42225 53.96832
>
> colMeans(tmp5,na.rm=TRUE)
[1] 112.48485 67.91996 70.21375 67.61173 71.74676 73.09994 72.45191
[8] 68.63108 69.45795 77.12795 68.16976 69.75234 71.94869 69.52211
[15] 74.32836 71.72906 71.83401 71.10615 66.45595 67.45247
> colSums(tmp5,na.rm=TRUE)
[1] 1124.8485 679.1996 702.1375 676.1173 717.4676 730.9994 724.5191
[8] 686.3108 694.5795 771.2795 681.6976 697.5234 719.4869 695.2211
[15] 743.2836 717.2906 718.3401 639.9553 664.5595 674.5247
> colVars(tmp5,na.rm=TRUE)
[1] 15590.15976 60.46782 40.05539 105.78793 106.17705 170.04042
[7] 54.35467 63.05105 86.11577 72.26171 107.79203 33.50085
[13] 104.25085 72.84953 94.28507 50.96460 93.91933 73.98209
[19] 142.96441 35.00180
> colSd(tmp5,na.rm=TRUE)
[1] 124.860561 7.776106 6.328933 10.285326 10.304225 13.039955
[7] 7.372562 7.940469 9.279858 8.500689 10.382294 5.787992
[13] 10.210331 8.535194 9.710050 7.138949 9.691199 8.601284
[19] 11.956773 5.916232
> colMax(tmp5,na.rm=TRUE)
[1] 466.94034 79.21696 85.16910 84.70787 97.25526 92.19530 84.81885
[8] 78.61658 82.37102 85.86089 83.97268 83.03620 91.41037 84.32645
[15] 89.95476 85.47230 86.62420 81.21513 86.37017 79.48383
> colMin(tmp5,na.rm=TRUE)
[1] 58.68971 57.16405 63.08520 56.05927 59.35169 54.72003 61.84723 56.66585
[9] 55.66040 61.85775 53.43713 62.37999 58.78933 53.86364 58.04232 63.10707
[17] 53.96832 59.61798 53.42225 59.61687
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.93272 67.19050 71.70408 71.11149 72.67111 67.30663 71.68989 NaN
[9] 68.15833 73.14335
> rowSums(tmp5,na.rm=TRUE)
[1] 1838.654 1343.810 1434.082 1422.230 1453.422 1346.133 1433.798 0.000
[9] 1363.167 1462.867
> rowVars(tmp5,na.rm=TRUE)
[1] 7840.86733 94.90580 74.25497 52.83077 102.06110 64.98614
[7] 75.90291 NA 71.72793 133.37783
> rowSd(tmp5,na.rm=TRUE)
[1] 88.548672 9.741961 8.617132 7.268478 10.102529 8.061398 8.712227
[8] NA 8.469234 11.548932
> rowMax(tmp5,na.rm=TRUE)
[1] 466.94034 87.70022 85.86089 86.62420 90.32120 85.47230 92.19530
[8] NA 84.24387 97.25526
> rowMin(tmp5,na.rm=TRUE)
[1] 61.54698 53.86364 53.62314 58.78933 53.43713 55.66040 56.20680 NA
[9] 53.42225 53.96832
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 117.53785 67.65609 70.77700 66.69265 71.49800 75.14216 71.07781
[8] 67.91097 68.85235 77.93214 66.41388 70.57149 69.78628 70.92651
[15] 74.89618 72.01760 71.19475 NaN 65.67991 67.68159
> colSums(tmp5,na.rm=TRUE)
[1] 1057.8406 608.9048 636.9930 600.2338 643.4820 676.2794 639.7003
[8] 611.1987 619.6711 701.3893 597.7249 635.1434 628.0765 638.3386
[15] 674.0656 648.1584 640.7528 0.0000 591.1192 609.1343
> colVars(tmp5,na.rm=TRUE)
[1] 17251.68547 67.24298 41.49328 109.50834 118.75300 144.37586
[7] 39.90716 65.09859 92.75427 74.01883 86.58099 30.13961
[13] 64.67708 59.76666 102.44352 56.39851 101.06196 NA
[19] 154.05983 38.78647
> colSd(tmp5,na.rm=TRUE)
[1] 131.345672 8.200181 6.441528 10.464623 10.897385 12.015651
[7] 6.317211 8.068369 9.630902 8.603420 9.304891 5.489956
[13] 8.042206 7.730890 10.121439 7.509894 10.052958 NA
[19] 12.412084 6.227879
> colMax(tmp5,na.rm=TRUE)
[1] 466.94034 79.21696 85.16910 84.70787 97.25526 92.19530 77.39495
[8] 78.61658 82.37102 85.86089 82.46143 83.03620 83.25769 84.32645
[15] 89.95476 85.47230 86.62420 -Inf 86.37017 79.48383
> colMin(tmp5,na.rm=TRUE)
[1] 58.68971 57.16405 63.08520 56.05927 59.35169 56.34914 61.84723 56.66585
[9] 55.66040 61.85775 53.43713 65.14702 58.78933 53.86364 58.04232 63.10707
[17] 53.96832 Inf 53.42225 59.61687
>
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 3
> which.col <- 1
> cat(which.row," ",which.col,"\n")
3 1
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> rowVars(tmp5,na.rm=TRUE)
[1] 187.95541 253.48742 159.21872 221.07274 258.11645 272.17099 79.59553
[8] 154.76527 185.15680 346.90482
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 187.95541 253.48742 159.21872 221.07274 258.11645 272.17099 79.59553
[8] 154.76527 185.15680 346.90482
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] -8.526513e-14 -1.421085e-14 1.136868e-13 4.263256e-14 7.105427e-14
[6] -5.684342e-14 5.684342e-14 -5.684342e-14 0.000000e+00 2.842171e-14
[11] -8.526513e-14 2.842171e-14 0.000000e+00 -2.842171e-14 1.136868e-13
[16] 4.547474e-13 1.421085e-13 -5.684342e-14 -2.842171e-14 5.684342e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
7 10
9 1
2 2
1 1
4 1
10 4
9 19
9 2
2 6
1 7
4 9
6 2
4 2
9 12
10 3
6 4
1 5
10 2
9 13
2 11
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 2.854718
> Min(tmp)
[1] -1.729279
> mean(tmp)
[1] 0.01847505
> Sum(tmp)
[1] 1.847505
> Var(tmp)
[1] 0.9051547
>
> rowMeans(tmp)
[1] 0.01847505
> rowSums(tmp)
[1] 1.847505
> rowVars(tmp)
[1] 0.9051547
> rowSd(tmp)
[1] 0.9513962
> rowMax(tmp)
[1] 2.854718
> rowMin(tmp)
[1] -1.729279
>
> colMeans(tmp)
[1] -0.15905637 0.26502212 0.11951455 -0.79159126 -0.41630846 1.22064282
[7] -0.41795823 -0.65877255 -0.06683307 -0.29831197 -0.79474155 -0.20335520
[13] -0.42769315 -1.15365771 -0.03320953 1.00252282 0.63033768 -0.32211581
[19] 0.28629932 -0.17176951 -0.32997092 -0.25457787 -0.29765489 0.66770672
[25] -0.07852845 0.33217759 0.68561061 1.18737390 1.05874643 -1.72927860
[31] 0.48898411 1.20416834 -0.78275567 -1.08144301 0.35956983 0.63026993
[37] 1.45352562 -0.52584536 0.19427974 0.79903991 0.17398942 1.48561641
[43] 0.09315980 0.62315875 -0.94559252 -0.59335848 0.16079982 -0.27021624
[49] -0.73744928 1.59733519 0.80095817 0.09929621 -1.68293743 0.32115155
[55] -1.57635239 -1.10255037 1.73940725 -0.49409891 -0.46533941 -1.13640454
[61] -0.37795186 0.35078537 -1.41695270 0.62052545 1.98188785 1.01742681
[67] -1.63375894 -1.17487638 -0.68721007 0.30574675 1.44550564 2.25043515
[73] 0.26007454 2.85471842 -1.24924337 -1.69028533 0.01853858 -1.14226676
[79] -1.65057055 1.40522795 1.04440680 -0.89599696 0.46041808 -0.94379327
[85] -0.21279723 0.82816505 -0.28086520 -0.63850897 0.64220760 0.47924063
[91] -0.89547474 0.61445995 1.53821575 1.03133238 -0.93355483 0.28461859
[97] -0.64771612 -0.04459671 0.15696276 -0.90791113
> colSums(tmp)
[1] -0.15905637 0.26502212 0.11951455 -0.79159126 -0.41630846 1.22064282
[7] -0.41795823 -0.65877255 -0.06683307 -0.29831197 -0.79474155 -0.20335520
[13] -0.42769315 -1.15365771 -0.03320953 1.00252282 0.63033768 -0.32211581
[19] 0.28629932 -0.17176951 -0.32997092 -0.25457787 -0.29765489 0.66770672
[25] -0.07852845 0.33217759 0.68561061 1.18737390 1.05874643 -1.72927860
[31] 0.48898411 1.20416834 -0.78275567 -1.08144301 0.35956983 0.63026993
[37] 1.45352562 -0.52584536 0.19427974 0.79903991 0.17398942 1.48561641
[43] 0.09315980 0.62315875 -0.94559252 -0.59335848 0.16079982 -0.27021624
[49] -0.73744928 1.59733519 0.80095817 0.09929621 -1.68293743 0.32115155
[55] -1.57635239 -1.10255037 1.73940725 -0.49409891 -0.46533941 -1.13640454
[61] -0.37795186 0.35078537 -1.41695270 0.62052545 1.98188785 1.01742681
[67] -1.63375894 -1.17487638 -0.68721007 0.30574675 1.44550564 2.25043515
[73] 0.26007454 2.85471842 -1.24924337 -1.69028533 0.01853858 -1.14226676
[79] -1.65057055 1.40522795 1.04440680 -0.89599696 0.46041808 -0.94379327
[85] -0.21279723 0.82816505 -0.28086520 -0.63850897 0.64220760 0.47924063
[91] -0.89547474 0.61445995 1.53821575 1.03133238 -0.93355483 0.28461859
[97] -0.64771612 -0.04459671 0.15696276 -0.90791113
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] -0.15905637 0.26502212 0.11951455 -0.79159126 -0.41630846 1.22064282
[7] -0.41795823 -0.65877255 -0.06683307 -0.29831197 -0.79474155 -0.20335520
[13] -0.42769315 -1.15365771 -0.03320953 1.00252282 0.63033768 -0.32211581
[19] 0.28629932 -0.17176951 -0.32997092 -0.25457787 -0.29765489 0.66770672
[25] -0.07852845 0.33217759 0.68561061 1.18737390 1.05874643 -1.72927860
[31] 0.48898411 1.20416834 -0.78275567 -1.08144301 0.35956983 0.63026993
[37] 1.45352562 -0.52584536 0.19427974 0.79903991 0.17398942 1.48561641
[43] 0.09315980 0.62315875 -0.94559252 -0.59335848 0.16079982 -0.27021624
[49] -0.73744928 1.59733519 0.80095817 0.09929621 -1.68293743 0.32115155
[55] -1.57635239 -1.10255037 1.73940725 -0.49409891 -0.46533941 -1.13640454
[61] -0.37795186 0.35078537 -1.41695270 0.62052545 1.98188785 1.01742681
[67] -1.63375894 -1.17487638 -0.68721007 0.30574675 1.44550564 2.25043515
[73] 0.26007454 2.85471842 -1.24924337 -1.69028533 0.01853858 -1.14226676
[79] -1.65057055 1.40522795 1.04440680 -0.89599696 0.46041808 -0.94379327
[85] -0.21279723 0.82816505 -0.28086520 -0.63850897 0.64220760 0.47924063
[91] -0.89547474 0.61445995 1.53821575 1.03133238 -0.93355483 0.28461859
[97] -0.64771612 -0.04459671 0.15696276 -0.90791113
> colMin(tmp)
[1] -0.15905637 0.26502212 0.11951455 -0.79159126 -0.41630846 1.22064282
[7] -0.41795823 -0.65877255 -0.06683307 -0.29831197 -0.79474155 -0.20335520
[13] -0.42769315 -1.15365771 -0.03320953 1.00252282 0.63033768 -0.32211581
[19] 0.28629932 -0.17176951 -0.32997092 -0.25457787 -0.29765489 0.66770672
[25] -0.07852845 0.33217759 0.68561061 1.18737390 1.05874643 -1.72927860
[31] 0.48898411 1.20416834 -0.78275567 -1.08144301 0.35956983 0.63026993
[37] 1.45352562 -0.52584536 0.19427974 0.79903991 0.17398942 1.48561641
[43] 0.09315980 0.62315875 -0.94559252 -0.59335848 0.16079982 -0.27021624
[49] -0.73744928 1.59733519 0.80095817 0.09929621 -1.68293743 0.32115155
[55] -1.57635239 -1.10255037 1.73940725 -0.49409891 -0.46533941 -1.13640454
[61] -0.37795186 0.35078537 -1.41695270 0.62052545 1.98188785 1.01742681
[67] -1.63375894 -1.17487638 -0.68721007 0.30574675 1.44550564 2.25043515
[73] 0.26007454 2.85471842 -1.24924337 -1.69028533 0.01853858 -1.14226676
[79] -1.65057055 1.40522795 1.04440680 -0.89599696 0.46041808 -0.94379327
[85] -0.21279723 0.82816505 -0.28086520 -0.63850897 0.64220760 0.47924063
[91] -0.89547474 0.61445995 1.53821575 1.03133238 -0.93355483 0.28461859
[97] -0.64771612 -0.04459671 0.15696276 -0.90791113
> colMedians(tmp)
[1] -0.15905637 0.26502212 0.11951455 -0.79159126 -0.41630846 1.22064282
[7] -0.41795823 -0.65877255 -0.06683307 -0.29831197 -0.79474155 -0.20335520
[13] -0.42769315 -1.15365771 -0.03320953 1.00252282 0.63033768 -0.32211581
[19] 0.28629932 -0.17176951 -0.32997092 -0.25457787 -0.29765489 0.66770672
[25] -0.07852845 0.33217759 0.68561061 1.18737390 1.05874643 -1.72927860
[31] 0.48898411 1.20416834 -0.78275567 -1.08144301 0.35956983 0.63026993
[37] 1.45352562 -0.52584536 0.19427974 0.79903991 0.17398942 1.48561641
[43] 0.09315980 0.62315875 -0.94559252 -0.59335848 0.16079982 -0.27021624
[49] -0.73744928 1.59733519 0.80095817 0.09929621 -1.68293743 0.32115155
[55] -1.57635239 -1.10255037 1.73940725 -0.49409891 -0.46533941 -1.13640454
[61] -0.37795186 0.35078537 -1.41695270 0.62052545 1.98188785 1.01742681
[67] -1.63375894 -1.17487638 -0.68721007 0.30574675 1.44550564 2.25043515
[73] 0.26007454 2.85471842 -1.24924337 -1.69028533 0.01853858 -1.14226676
[79] -1.65057055 1.40522795 1.04440680 -0.89599696 0.46041808 -0.94379327
[85] -0.21279723 0.82816505 -0.28086520 -0.63850897 0.64220760 0.47924063
[91] -0.89547474 0.61445995 1.53821575 1.03133238 -0.93355483 0.28461859
[97] -0.64771612 -0.04459671 0.15696276 -0.90791113
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.1590564 0.2650221 0.1195145 -0.7915913 -0.4163085 1.220643 -0.4179582
[2,] -0.1590564 0.2650221 0.1195145 -0.7915913 -0.4163085 1.220643 -0.4179582
[,8] [,9] [,10] [,11] [,12] [,13]
[1,] -0.6587726 -0.06683307 -0.298312 -0.7947415 -0.2033552 -0.4276932
[2,] -0.6587726 -0.06683307 -0.298312 -0.7947415 -0.2033552 -0.4276932
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] -1.153658 -0.03320953 1.002523 0.6303377 -0.3221158 0.2862993 -0.1717695
[2,] -1.153658 -0.03320953 1.002523 0.6303377 -0.3221158 0.2862993 -0.1717695
[,21] [,22] [,23] [,24] [,25] [,26] [,27]
[1,] -0.3299709 -0.2545779 -0.2976549 0.6677067 -0.07852845 0.3321776 0.6856106
[2,] -0.3299709 -0.2545779 -0.2976549 0.6677067 -0.07852845 0.3321776 0.6856106
[,28] [,29] [,30] [,31] [,32] [,33] [,34]
[1,] 1.187374 1.058746 -1.729279 0.4889841 1.204168 -0.7827557 -1.081443
[2,] 1.187374 1.058746 -1.729279 0.4889841 1.204168 -0.7827557 -1.081443
[,35] [,36] [,37] [,38] [,39] [,40] [,41]
[1,] 0.3595698 0.6302699 1.453526 -0.5258454 0.1942797 0.7990399 0.1739894
[2,] 0.3595698 0.6302699 1.453526 -0.5258454 0.1942797 0.7990399 0.1739894
[,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] 1.485616 0.0931598 0.6231588 -0.9455925 -0.5933585 0.1607998 -0.2702162
[2,] 1.485616 0.0931598 0.6231588 -0.9455925 -0.5933585 0.1607998 -0.2702162
[,49] [,50] [,51] [,52] [,53] [,54] [,55]
[1,] -0.7374493 1.597335 0.8009582 0.09929621 -1.682937 0.3211515 -1.576352
[2,] -0.7374493 1.597335 0.8009582 0.09929621 -1.682937 0.3211515 -1.576352
[,56] [,57] [,58] [,59] [,60] [,61] [,62]
[1,] -1.10255 1.739407 -0.4940989 -0.4653394 -1.136405 -0.3779519 0.3507854
[2,] -1.10255 1.739407 -0.4940989 -0.4653394 -1.136405 -0.3779519 0.3507854
[,63] [,64] [,65] [,66] [,67] [,68] [,69]
[1,] -1.416953 0.6205254 1.981888 1.017427 -1.633759 -1.174876 -0.6872101
[2,] -1.416953 0.6205254 1.981888 1.017427 -1.633759 -1.174876 -0.6872101
[,70] [,71] [,72] [,73] [,74] [,75] [,76]
[1,] 0.3057468 1.445506 2.250435 0.2600745 2.854718 -1.249243 -1.690285
[2,] 0.3057468 1.445506 2.250435 0.2600745 2.854718 -1.249243 -1.690285
[,77] [,78] [,79] [,80] [,81] [,82] [,83]
[1,] 0.01853858 -1.142267 -1.650571 1.405228 1.044407 -0.895997 0.4604181
[2,] 0.01853858 -1.142267 -1.650571 1.405228 1.044407 -0.895997 0.4604181
[,84] [,85] [,86] [,87] [,88] [,89] [,90]
[1,] -0.9437933 -0.2127972 0.828165 -0.2808652 -0.638509 0.6422076 0.4792406
[2,] -0.9437933 -0.2127972 0.828165 -0.2808652 -0.638509 0.6422076 0.4792406
[,91] [,92] [,93] [,94] [,95] [,96] [,97]
[1,] -0.8954747 0.6144599 1.538216 1.031332 -0.9335548 0.2846186 -0.6477161
[2,] -0.8954747 0.6144599 1.538216 1.031332 -0.9335548 0.2846186 -0.6477161
[,98] [,99] [,100]
[1,] -0.04459671 0.1569628 -0.9079111
[2,] -0.04459671 0.1569628 -0.9079111
>
>
> Max(tmp2)
[1] 2.678467
> Min(tmp2)
[1] -2.265665
> mean(tmp2)
[1] 0.002614417
> Sum(tmp2)
[1] 0.2614417
> Var(tmp2)
[1] 1.167887
>
> rowMeans(tmp2)
[1] 0.23035091 -0.06402257 -1.25846877 -0.61423355 -0.57408879 0.72725964
[7] 0.13784373 0.87412300 -0.40497264 -0.67428073 0.91995510 -0.57770597
[13] -0.21495502 0.21963041 -1.44158379 0.71550539 -1.04835543 1.26668839
[19] -0.46225745 -1.44603703 0.39956643 0.09735128 2.67846694 -1.20432614
[25] 0.25179393 0.31155750 -0.38159040 0.06881937 0.51682968 -0.86151997
[31] 0.62519127 1.43654972 0.46452124 1.19586654 0.76378735 0.77494525
[37] -0.54065242 1.39864612 -0.61202102 1.28405590 -0.24842419 -0.57188786
[43] 0.27695139 -2.17242920 -0.69029404 1.15201601 2.50189670 0.24810447
[49] -0.02243976 1.02046502 -0.04158084 1.36346384 1.49328911 -1.85077698
[55] -1.90411276 -1.24873620 -0.38303874 1.51229647 0.56562026 -0.54132085
[61] 0.18395725 -1.60863588 -1.75176488 -0.78111737 0.51486665 1.37671283
[67] -1.31519998 -2.26566509 -0.20732865 -1.73024627 1.91198681 0.29957151
[73] -0.42519166 -1.04144270 1.65119396 0.65637476 -1.33710549 0.39569491
[79] -0.37351322 -0.04428053 0.89299970 0.27419102 0.05257417 -1.25940590
[85] 1.19945244 0.56696023 -0.20912215 0.55506359 0.96207193 -2.16896357
[91] -1.75800108 0.70418372 0.97972546 0.54162286 1.32989556 0.65162019
[97] -1.31051080 -0.34739114 -1.98223456 1.04054784
> rowSums(tmp2)
[1] 0.23035091 -0.06402257 -1.25846877 -0.61423355 -0.57408879 0.72725964
[7] 0.13784373 0.87412300 -0.40497264 -0.67428073 0.91995510 -0.57770597
[13] -0.21495502 0.21963041 -1.44158379 0.71550539 -1.04835543 1.26668839
[19] -0.46225745 -1.44603703 0.39956643 0.09735128 2.67846694 -1.20432614
[25] 0.25179393 0.31155750 -0.38159040 0.06881937 0.51682968 -0.86151997
[31] 0.62519127 1.43654972 0.46452124 1.19586654 0.76378735 0.77494525
[37] -0.54065242 1.39864612 -0.61202102 1.28405590 -0.24842419 -0.57188786
[43] 0.27695139 -2.17242920 -0.69029404 1.15201601 2.50189670 0.24810447
[49] -0.02243976 1.02046502 -0.04158084 1.36346384 1.49328911 -1.85077698
[55] -1.90411276 -1.24873620 -0.38303874 1.51229647 0.56562026 -0.54132085
[61] 0.18395725 -1.60863588 -1.75176488 -0.78111737 0.51486665 1.37671283
[67] -1.31519998 -2.26566509 -0.20732865 -1.73024627 1.91198681 0.29957151
[73] -0.42519166 -1.04144270 1.65119396 0.65637476 -1.33710549 0.39569491
[79] -0.37351322 -0.04428053 0.89299970 0.27419102 0.05257417 -1.25940590
[85] 1.19945244 0.56696023 -0.20912215 0.55506359 0.96207193 -2.16896357
[91] -1.75800108 0.70418372 0.97972546 0.54162286 1.32989556 0.65162019
[97] -1.31051080 -0.34739114 -1.98223456 1.04054784
> rowVars(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowSd(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowMax(tmp2)
[1] 0.23035091 -0.06402257 -1.25846877 -0.61423355 -0.57408879 0.72725964
[7] 0.13784373 0.87412300 -0.40497264 -0.67428073 0.91995510 -0.57770597
[13] -0.21495502 0.21963041 -1.44158379 0.71550539 -1.04835543 1.26668839
[19] -0.46225745 -1.44603703 0.39956643 0.09735128 2.67846694 -1.20432614
[25] 0.25179393 0.31155750 -0.38159040 0.06881937 0.51682968 -0.86151997
[31] 0.62519127 1.43654972 0.46452124 1.19586654 0.76378735 0.77494525
[37] -0.54065242 1.39864612 -0.61202102 1.28405590 -0.24842419 -0.57188786
[43] 0.27695139 -2.17242920 -0.69029404 1.15201601 2.50189670 0.24810447
[49] -0.02243976 1.02046502 -0.04158084 1.36346384 1.49328911 -1.85077698
[55] -1.90411276 -1.24873620 -0.38303874 1.51229647 0.56562026 -0.54132085
[61] 0.18395725 -1.60863588 -1.75176488 -0.78111737 0.51486665 1.37671283
[67] -1.31519998 -2.26566509 -0.20732865 -1.73024627 1.91198681 0.29957151
[73] -0.42519166 -1.04144270 1.65119396 0.65637476 -1.33710549 0.39569491
[79] -0.37351322 -0.04428053 0.89299970 0.27419102 0.05257417 -1.25940590
[85] 1.19945244 0.56696023 -0.20912215 0.55506359 0.96207193 -2.16896357
[91] -1.75800108 0.70418372 0.97972546 0.54162286 1.32989556 0.65162019
[97] -1.31051080 -0.34739114 -1.98223456 1.04054784
> rowMin(tmp2)
[1] 0.23035091 -0.06402257 -1.25846877 -0.61423355 -0.57408879 0.72725964
[7] 0.13784373 0.87412300 -0.40497264 -0.67428073 0.91995510 -0.57770597
[13] -0.21495502 0.21963041 -1.44158379 0.71550539 -1.04835543 1.26668839
[19] -0.46225745 -1.44603703 0.39956643 0.09735128 2.67846694 -1.20432614
[25] 0.25179393 0.31155750 -0.38159040 0.06881937 0.51682968 -0.86151997
[31] 0.62519127 1.43654972 0.46452124 1.19586654 0.76378735 0.77494525
[37] -0.54065242 1.39864612 -0.61202102 1.28405590 -0.24842419 -0.57188786
[43] 0.27695139 -2.17242920 -0.69029404 1.15201601 2.50189670 0.24810447
[49] -0.02243976 1.02046502 -0.04158084 1.36346384 1.49328911 -1.85077698
[55] -1.90411276 -1.24873620 -0.38303874 1.51229647 0.56562026 -0.54132085
[61] 0.18395725 -1.60863588 -1.75176488 -0.78111737 0.51486665 1.37671283
[67] -1.31519998 -2.26566509 -0.20732865 -1.73024627 1.91198681 0.29957151
[73] -0.42519166 -1.04144270 1.65119396 0.65637476 -1.33710549 0.39569491
[79] -0.37351322 -0.04428053 0.89299970 0.27419102 0.05257417 -1.25940590
[85] 1.19945244 0.56696023 -0.20912215 0.55506359 0.96207193 -2.16896357
[91] -1.75800108 0.70418372 0.97972546 0.54162286 1.32989556 0.65162019
[97] -1.31051080 -0.34739114 -1.98223456 1.04054784
>
> colMeans(tmp2)
[1] 0.002614417
> colSums(tmp2)
[1] 0.2614417
> colVars(tmp2)
[1] 1.167887
> colSd(tmp2)
[1] 1.080688
> colMax(tmp2)
[1] 2.678467
> colMin(tmp2)
[1] -2.265665
> colMedians(tmp2)
[1] 0.1175975
> colRanges(tmp2)
[,1]
[1,] -2.265665
[2,] 2.678467
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] -2.2799041 -3.3097878 -0.8012412 1.2463992 0.4170415 1.3605951
[7] 4.0682081 -5.3960406 1.1880793 -0.5646853
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.1500057
[2,] -0.9826718
[3,] -0.1514872
[4,] 0.1728165
[5,] 2.6750163
>
> rowApply(tmp,sum)
[1] -6.3380591 -1.5690317 -0.8234809 4.8451629 1.8140573 -2.8472984
[7] -2.1182531 1.1136738 2.1089984 -0.2571049
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 2 6 4 10 6 2 7 5 1 5
[2,] 6 9 5 2 3 5 4 9 2 1
[3,] 5 3 9 1 10 1 10 2 7 8
[4,] 1 2 8 9 1 9 8 7 5 10
[5,] 4 10 2 5 9 3 6 10 4 3
[6,] 8 7 10 4 4 10 3 3 6 2
[7,] 9 8 6 8 2 8 9 8 3 7
[8,] 7 1 1 6 7 6 1 4 8 4
[9,] 10 5 3 3 8 7 2 6 10 6
[10,] 3 4 7 7 5 4 5 1 9 9
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 3.0232855 -1.3396683 -3.4908536 -0.4300454 0.8385368 -4.7085967
[7] 4.6084504 -2.7706976 -1.4242978 0.1690770 1.3820152 0.8900509
[13] -1.0106592 -2.0809672 0.9176927 0.2514231 -3.6515010 1.5752638
[19] 0.1769017 -1.0278502
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.6812903
[2,] -0.5470590
[3,] 1.1183857
[4,] 1.2985336
[5,] 1.8347154
>
> rowApply(tmp,sum)
[1] -4.244454 3.281822 -5.282311 -3.000595 1.143099
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 18 6 20 6 18
[2,] 3 17 14 10 3
[3,] 8 2 9 11 2
[4,] 12 5 18 13 7
[5,] 19 13 17 3 8
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1.1183857 -1.1818669 -0.4316619 -0.16442222 1.1279177 -1.5937100
[2,] -0.5470590 0.8758636 -0.8378174 -0.56192187 0.5792622 -1.1184522
[3,] 1.8347154 0.1681476 -0.5317361 0.78078874 0.6539802 -0.7173207
[4,] -0.6812903 -0.3207223 -0.2374749 0.09518991 -1.1186747 -1.5694422
[5,] 1.2985336 -0.8810903 -1.4521633 -0.57967992 -0.4039485 0.2903284
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 1.4100063 -1.5016410 0.31963482 -1.0222487 1.0389567 0.80617354
[2,] 0.8046909 0.9298830 0.05695761 0.6569261 1.5178472 0.16353312
[3,] 1.4960171 -2.5711940 -0.29802430 0.3965589 -0.1943122 0.20710536
[4,] -0.3284937 0.2461322 -0.71807734 -1.2744378 1.0286947 -0.33328290
[5,] 1.2262299 0.1261221 -0.78478856 1.4122785 -2.0091711 0.04652176
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.4226958 -0.7749351 -1.102986885 -1.0760691 -0.1412744 -0.02235955
[2,] 0.2170090 0.7512503 0.378412390 -0.4994442 -0.5742774 0.88485778
[3,] -0.6584324 -1.1842095 0.001361884 -0.5511691 -1.2906748 -1.23889203
[4,] 0.7071807 -0.6118109 0.421742785 1.6213169 -0.8591842 0.13713051
[5,] -0.8537207 -0.2612620 1.219162481 0.7567887 -0.7860902 1.81452706
[,19] [,20]
[1,] -0.3580318 -0.27162524
[2,] -0.6428923 0.24719280
[3,] -0.5205967 -1.06442447
[4,] 0.7620687 0.03283936
[5,] 0.9363538 0.02816736
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 653 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 565 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 -1.862171 -2.066061 0.4141304 0.2466556 -0.7139864 -0.296387 2.480434
col8 col9 col10 col11 col12 col13 col14
row1 -0.3751746 -0.1410131 -0.05769665 0.07505623 1.420736 1.499347 -0.6825858
col15 col16 col17 col18 col19 col20
row1 0.9973362 -0.6110202 -0.4034463 -0.7432983 -0.6073838 -0.5628212
> tmp[,"col10"]
col10
row1 -0.05769665
row2 -0.98147494
row3 0.68535152
row4 0.53017838
row5 -0.43103251
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -1.862171 -2.066061 0.4141304 0.2466556 -0.7139864 -0.2963870 2.480434
row5 -1.408136 -1.334449 -0.2529986 1.5624941 0.1208563 0.8721172 2.850867
col8 col9 col10 col11 col12 col13
row1 -0.3751746 -0.1410131 -0.05769665 0.07505623 1.4207358 1.4993465
row5 -0.7123346 -0.3981545 -0.43103251 -0.97800263 -0.1587215 -0.5301181
col14 col15 col16 col17 col18 col19
row1 -0.6825858 0.9973362 -0.6110202 -0.4034463 -0.7432983 -0.6073838
row5 -1.0384323 0.7701307 1.3885157 1.2992563 0.6720105 -0.6206506
col20
row1 -0.5628212
row5 2.2038613
> tmp[,c("col6","col20")]
col6 col20
row1 -0.29638698 -0.5628212
row2 0.09199817 -1.6359361
row3 -0.88874299 -0.5911503
row4 -1.34894239 0.3558560
row5 0.87211716 2.2038613
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.2963870 -0.5628212
row5 0.8721172 2.2038613
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.54582 48.53681 50.15118 48.12866 50.69408 104.7609 49.82289 48.8656
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.20309 50.17187 50.7998 48.03415 48.45602 51.35675 50.25066 48.836
col17 col18 col19 col20
row1 49.62286 50.04055 52.09136 104.1296
> tmp[,"col10"]
col10
row1 50.17187
row2 31.24134
row3 28.70257
row4 29.23521
row5 49.76808
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.54582 48.53681 50.15118 48.12866 50.69408 104.7609 49.82289 48.86560
row5 50.86515 50.80533 51.37674 52.56739 49.41632 104.7806 51.03312 51.16921
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.20309 50.17187 50.79980 48.03415 48.45602 51.35675 50.25066 48.83600
row5 48.68843 49.76808 49.05289 49.90220 50.27830 49.92919 49.32571 50.84484
col17 col18 col19 col20
row1 49.62286 50.04055 52.09136 104.1296
row5 50.13539 49.70492 48.74909 106.4491
> tmp[,c("col6","col20")]
col6 col20
row1 104.76089 104.12963
row2 75.38750 75.14987
row3 73.47350 75.65228
row4 73.99042 74.94183
row5 104.78059 106.44908
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.7609 104.1296
row5 104.7806 106.4491
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.7609 104.1296
row5 104.7806 106.4491
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.36118848
[2,] -0.02820572
[3,] 1.75086066
[4,] 0.25993807
[5,] -1.14241695
> tmp[,c("col17","col7")]
col17 col7
[1,] -2.0263057 2.0790671
[2,] 0.6821734 0.6018805
[3,] -0.7890662 -2.4496967
[4,] 1.5181875 -1.2588530
[5,] -0.9072778 0.5306074
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -2.0721538 -0.8388668
[2,] -0.0159332 1.9326072
[3,] 0.1338602 -1.1956190
[4,] 0.1988933 0.9094994
[5,] 1.4533822 2.0333994
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -2.072154
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -2.0721538
[2,] -0.0159332
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row3 1.3379940 0.01043756 1.359817 0.3037827 -1.529373 -0.7939523 -0.4927879
row1 0.1696683 -0.48370107 1.060707 -0.0709972 0.805883 -0.7663159 -0.1698374
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row3 0.1840363 -1.0328779 0.5979568 0.5342957 -0.4406757 -1.1728301 -0.3071391
row1 1.9106186 0.2623691 0.3620428 -0.2073530 0.6412628 0.4002036 1.3831151
[,15] [,16] [,17] [,18] [,19] [,20]
row3 1.403973 0.2713096 -1.069386 0.7932499 0.5409879 -0.001423782
row1 1.421430 -0.8195503 1.121704 0.6834322 0.8094598 -0.483855408
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -1.308697 -0.5581171 0.8313412 -1.729388 -0.1080287 -0.322672 -1.388168
[,8] [,9] [,10]
row2 0.3250956 0.3295698 -1.767139
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.9729621 -0.7288396 -0.2882252 0.9360572 0.331428 1.221795 -0.1633918
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.7125445 0.8901328 -1.199096 0.4037848 -1.297397 1.167793 0.05412856
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.1566 0.5838397 -0.1503491 -0.7990362 -1.963049 0.7975775
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> colnames(tmp) <- NULL
> rownames(tmp) <- NULL
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
> dimnames(tmp) <- NULL
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
> dimnames(tmp) <- NULL
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
NULL
>
> dimnames(tmp) <- list(NULL,c(colnames(tmp,do.NULL=FALSE)))
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
>
> ###
> ### Testing logical indexing
> ###
> ###
>
> tmp <- createBufferedMatrix(230,15)
> tmp[1:230,1:15] <- rnorm(230*15)
> x <-tmp[1:230,1:15]
>
> for (rep in 1:10){
+ which.cols <- sample(c(TRUE,FALSE),15,replace=T)
+ which.rows <- sample(c(TRUE,FALSE),230,replace=T)
+
+ if (!all(tmp[which.rows,which.cols] == x[which.rows,which.cols])){
+ stop("No agreement when logical indexing\n")
+ }
+
+ if (!all(subBufferedMatrix(tmp,,which.cols)[,1:sum(which.cols)] == x[,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix cols\n")
+ }
+ if (!all(subBufferedMatrix(tmp,which.rows,)[1:sum(which.rows),] == x[which.rows,])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows\n")
+ }
+
+
+ if (!all(subBufferedMatrix(tmp,which.rows,which.cols)[1:sum(which.rows),1:sum(which.cols)]== x[which.rows,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows and columns\n")
+ }
+ }
>
>
> ##
> ## Test the ReadOnlyMode
> ##
>
> ReadOnlyMode(tmp)
<pointer: 0x563927093570>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM25d90066a81bcc"
[2] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM25d90072069dd4"
[3] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM25d90029b78603"
[4] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM25d900561e997f"
[5] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM25d90057942c71"
[6] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM25d9002f6b467a"
[7] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM25d9002124bed7"
[8] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM25d90070973b3e"
[9] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM25d9001cd701bb"
[10] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM25d90060c6c18f"
[11] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM25d90073b663d"
[12] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM25d900ee82d64"
[13] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM25d900727f7023"
[14] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM25d9006f8fde64"
[15] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM25d9003d678607"
>
>
> ### testing coercion functions
> ###
>
> tmp <- as(tmp,"matrix")
> tmp <- as(tmp,"BufferedMatrix")
>
>
>
> ### testing whether can move storage from one location to another
>
> MoveStorageDirectory(tmp,"NewDirectory",full.path=FALSE)
<pointer: 0x563927c50b60>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x563927c50b60>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x563927c50b60>
> rowMedians(tmp)
[1] -0.032000016 -0.063399757 0.132645182 0.095377927 0.257256570
[6] -0.194951473 0.697541003 -0.276392334 0.376986188 0.097718548
[11] -0.277729854 -0.341426834 0.463467337 0.237844116 0.792315410
[16] 0.139009836 -0.201012119 -0.311007466 0.326161046 0.057145514
[21] -0.297208560 0.153364533 0.043434537 -0.018158414 -0.214094582
[26] -0.244618529 0.210299720 0.039351169 -0.262530347 0.395894267
[31] -0.237787417 0.394342256 -0.127772180 0.386787233 0.231964563
[36] 0.257526942 -0.198895004 -0.123596742 -0.110037398 -0.111194920
[41] 0.275866092 0.267800868 0.166765118 -0.347855659 0.709114828
[46] -0.289226053 -0.231720663 0.417546292 0.366600484 -0.028746656
[51] 0.268566591 -0.251580511 0.130107360 -0.174612090 0.096456991
[56] -0.498463407 0.480217638 0.070117102 -0.060289426 0.386341938
[61] -0.265591193 0.195975473 -0.200087043 -0.048588460 0.497095126
[66] -0.324036753 0.237970384 -0.093681078 0.066038184 -0.317691586
[71] -0.121150877 -0.008821940 -0.208993243 -0.131866453 0.067956735
[76] -0.090242795 -0.332915641 -0.388219911 -0.049079585 -1.192632506
[81] -0.326903366 -0.101798026 -0.041220514 -0.359112057 -0.022407356
[86] 0.294197818 0.012589960 0.599060621 0.207885861 -0.142657904
[91] -0.210064615 0.240138324 -0.309544885 0.107710295 0.052799490
[96] 0.340311100 0.254513000 0.096290726 0.105154846 -0.645393841
[101] -0.061670602 -0.369458260 -0.294889659 0.283149069 0.136184753
[106] 0.003428363 -0.025395247 -0.423556196 0.448256744 -0.072592454
[111] -0.267046843 -0.179941124 0.230646976 0.169739764 -0.029518510
[116] 0.565744762 -0.321719995 -0.190137856 -0.739006998 -0.058355093
[121] -0.195838854 -0.552707830 -0.188605830 0.077866110 -0.243434981
[126] -0.131332455 -0.521404075 -0.148140409 0.262500121 0.395502443
[131] 0.768817780 0.238969536 0.378114131 -0.509491755 0.107330584
[136] -0.360390899 -0.002947246 0.848370599 -0.019463207 -0.036755793
[141] 0.506455007 0.816748625 -0.137576956 0.366330176 0.208145742
[146] 0.358179664 -0.068487277 0.237662942 -0.155242695 0.621690280
[151] 0.513835050 0.434660168 -0.093007941 0.115837050 -0.085627914
[156] 0.207387118 -0.060331181 -0.221302719 0.009948933 0.313641886
[161] 0.026238250 0.193606054 -0.623141647 -0.219704340 0.052413940
[166] -0.425469760 -0.585246402 0.107893421 0.246119957 -0.142303761
[171] 0.260703782 -0.002542344 -0.278006428 0.515400705 0.303130606
[176] -0.303299307 0.323385709 0.276105173 -0.738770093 0.507262132
[181] -0.154300121 0.155084048 -0.176523822 -0.160504548 -0.117663566
[186] -0.139814634 -0.227392359 0.341380214 -0.159661637 -0.176836810
[191] 0.206029833 0.270858896 0.355420592 0.325424583 0.035421059
[196] 0.026211359 -0.105985807 0.082173966 0.071172170 -0.226436277
[201] 0.966721408 -0.327495461 0.067952819 0.492940871 0.165725219
[206] -0.174780331 0.376889295 -0.205065413 0.514759769 -0.132108933
[211] -0.263636470 -0.225610498 0.189360577 0.057142790 -0.238778559
[216] 0.156474654 0.201176912 0.085428957 -0.355867049 -0.496184326
[221] -0.096946272 0.151849125 0.004321072 0.107117250 0.194631654
[226] 0.122559616 -0.175703914 -0.419480026 0.452655212 0.352733044
>
> proc.time()
user system elapsed
1.248 0.654 1.891
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> prefix <- "dbmtest"
> directory <- getwd()
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x5b56ad761370>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x5b56ad761370>
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x5b56ad761370>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000 0.000000 0.000000 0.000000 0.000000
<pointer: 0x5b56ad761370>
> rm(P)
>
> #P <- .Call("R_bm_Destroy",P)
> #.Call("R_bm_Destroy",P)
> #.Call("R_bm_Test_C",P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 0
Buffer Rows: 1
Buffer Cols: 1
Printing Values
<pointer: 0x5b56ad7491c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b56ad7491c0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 1
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000
0.000000
0.000000
0.000000
0.000000
<pointer: 0x5b56ad7491c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b56ad7491c0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x5b56ad7491c0>
> rm(P)
>
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b56ada2c120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b56ada2c120>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x5b56ada2c120>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5b56ada2c120>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x5b56ada2c120>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x5b56ada2c120>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x5b56ada2c120>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x5b56ada2c120>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x5b56ada2c120>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b56ac77c390>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x5b56ac77c390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b56ac77c390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b56ac77c390>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile25d9ba1baad762" "BufferedMatrixFile25d9ba2e4e0a68"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile25d9ba1baad762" "BufferedMatrixFile25d9ba2e4e0a68"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b56ac6733d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b56ac6733d0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5b56ac6733d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5b56ac6733d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x5b56ac6733d0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x5b56ac6733d0>
> .Call("R_bm_isRowMode",P)
[1] FALSE
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b56ae1a8fa0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b56ae1a8fa0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5b56ae1a8fa0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x5b56ae1a8fa0>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x5b56ac980ff0>
> .Call("R_bm_getValue",P,3,3)
[1] 6
>
> .Call("R_bm_getValue",P,100000,10000)
[1] NA
> .Call("R_bm_setValue",P,3,3,12345.0)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 12345.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x5b56ac980ff0>
> rm(P)
>
> proc.time()
user system elapsed
0.239 0.045 0.273
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.231 0.054 0.274