Multiple platform build/check report for BioC 3.11 - CHECK report for cmapR on tokay2

Package: cmapR

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cmapR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings cmapR_1.0.0.tar.gz

StartedAt: 2020-10-17 02:44:09 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 02:49:09 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 299.7 seconds

RetCode: 0

Status: WARNINGS

CheckDir: cmapR.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cmapR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings cmapR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/cmapR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cmapR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cmapR' version '1.0.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .dockerignore
  docs/build/html/.buildinfo
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'cmapR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   2.1Mb
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ... NOTE
subset_gct,GCT: warning in meta(g, dim = "col"): partial argument match
  of 'dim' to 'dimension'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'ids<-' 'mat<-' 'meta<-'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/cmapR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/cmapR_1.0.0.tar.gz && rm -rf cmapR.buildbin-libdir && mkdir cmapR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cmapR.buildbin-libdir cmapR_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL cmapR_1.0.0.zip && rm cmapR_1.0.0.tar.gz cmapR_1.0.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3652k  100 3652k    0     0  38.6M      0 --:--:-- --:--:-- --:--:-- 41.9M

install for i386

* installing *source* package 'cmapR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cmapR'
    finding HTML links ... done
    GCT-class                               html  
    GCT                                     html  
    align_matrices                          html  
    annotate_gct                            html  
    append_dim                              html  
    cdesc_char                              html  
    check_colnames                          html  
    check_dups                              html  
    distil                                  html  
    ds                                      html  
    extract_gct                             html  
    fix_datatypes                           html  
    gene_set                                html  
    ids                                     html  
    is.wholenumber                          html  
    kd_gct                                  html  
    lxb2mat                                 html  
    mat                                     html  
    melt_gct                                html  
    finding level-2 HTML links ... done

    merge_gct                               html  
    merge_with_precedence                   html  
    meta                                    html  
    na_pad_matrix                           html  
    parse_gctx                              html  
    parse_gmt                               html  
    parse_gmx                               html  
    parse_grp                               html  
    process_ids                             html  
    rank_gct                                html  
    read_gctx_ids                           html  
    read_gctx_meta                          html  
    robust_zscore                           html  
    subset_gct                              html  
    subset_to_ids                           html  
    threshold                               html  
    transpose_gct                           html  
    update_gctx                             html  
    write_gct                               html  
    write_gctx                              html  
    write_gctx_meta                         html  
    write_gmt                               html  
    write_grp                               html  
    write_tbl                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'cmapR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cmapR' as cmapR_1.0.0.zip
* DONE (cmapR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'cmapR' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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(testthat)
> library(cmapR)
> 
> test_check("cmapR")
Saving file to  foo.gct 
Dimensions of matrix: [10x5]
Setting precision to 4
Saved.
Saving file to  foo.gct 
Dimensions of matrix: [10x5]
Setting precision to 4
Saved.
Saving file to  ./foo_n272x978.gct 
Dimensions of matrix: [978x272]
Setting precision to 4
Saved.
== testthat results  ===========================================================
[ OK: 165 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  16.84    1.82   18.01


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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(testthat)
> library(cmapR)
> 
> test_check("cmapR")
Saving file to  foo.gct 
Dimensions of matrix: [10x5]
Setting precision to 4
Saved.
Saving file to  foo.gct 
Dimensions of matrix: [10x5]
Setting precision to 4
Saved.
Saving file to  ./foo_n272x978.gct 
Dimensions of matrix: [978x272]
Setting precision to 4
Saved.
== testthat results  ===========================================================
[ OK: 165 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  21.23    1.34   21.90

name	user	system	elapsed
GCT	0.21	0.03	0.23
align_matrices	0.01	0.00	0.02
annotate_gct	0.14	0.08	0.21
append_dim	0	0	0
check_colnames	0.00	0.02	0.02
check_dups	0	0	0
distil	0	0	0
extract_gct	0.25	0.00	0.25
fix_datatypes	0.07	0.00	0.06
ids	0.03	0.00	0.03
is.wholenumber	0	0	0
lxb2mat	0.01	0.02	1.14
mat	0.02	0.00	0.02
melt_gct	2.36	0.34	2.12
merge_gct	0.22	0.02	0.24
merge_with_precedence	0	0	0
meta	0	0	0
na_pad_matrix	0	0	0
parse_gctx	0.38	0.00	0.38
parse_gmt	0.06	0.00	0.06
parse_gmx	0.03	0.00	0.03
parse_grp	0	0	0
process_ids	0.01	0.00	0.01
rank_gct	0.27	0.00	0.27
read_gctx_ids	0.01	0.00	0.01
read_gctx_meta	0.21	0.00	0.21
robust_zscore	0	0	0
subset_gct	0.10	0.00	0.09
threshold	0	0	0
transpose_gct	0.14	0.00	0.15
update_gctx	0	0	0
write_gct	1.86	0.50	2.35
write_gctx	0.18	0.11	0.41
write_gctx_meta	0	0	0
write_gmt	0	0	0
write_grp	0	0	0
write_tbl	0	0	0

name	user	system	elapsed
GCT	0.18	0.03	0.20
align_matrices	0.00	0.02	0.02
annotate_gct	0.23	0.03	0.27
append_dim	0	0	0
check_colnames	0	0	0
check_dups	0	0	0
distil	0	0	0
extract_gct	0.12	0.01	0.14
fix_datatypes	0.04	0.00	0.03
ids	0.02	0.00	0.02
is.wholenumber	0	0	0
lxb2mat	0.01	0.00	0.01
mat	0.02	0.00	0.02
melt_gct	3.28	0.32	3.14
merge_gct	0.23	0.00	0.24
merge_with_precedence	0.02	0.00	0.01
meta	0	0	0
na_pad_matrix	0	0	0
parse_gctx	0.22	0.03	0.25
parse_gmt	0.03	0.00	0.03
parse_gmx	0.00	0.03	0.03
parse_grp	0	0	0
process_ids	0.02	0.00	0.02
rank_gct	0.14	0.00	0.14
read_gctx_ids	0.01	0.00	0.02
read_gctx_meta	0.10	0.04	0.14
robust_zscore	0	0	0
subset_gct	0.06	0.00	0.06
threshold	0	0	0
transpose_gct	0.09	0.00	0.09
update_gctx	0	0	0
write_gct	1.77	0.32	2.28
write_gctx	0.25	0.01	2.03
write_gctx_meta	0	0	0
write_gmt	0	0	0
write_grp	0	0	0
write_tbl	0	0	0

CHECK report for cmapR on tokay2

Summary

Command output

Installation output

Tests output

Example timings