Felix G.M. Ernst
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/RNAmodR |
| Branch: RELEASE_3_11 |
| Last Commit: c0299cf |
| Last Changed Date: 2020-08-30 07:11:07 -0400 (Sun, 30 Aug 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:40 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE RNAmodR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1508/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RNAmodR 1.2.3 Felix G.M. Ernst
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: RNAmodR |
| Version: 1.2.3 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNAmodR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RNAmodR_1.2.3.tar.gz |
| StartedAt: 2020-10-17 07:37:50 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 07:57:49 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 1198.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RNAmodR.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNAmodR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RNAmodR_1.2.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/RNAmodR.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 'RNAmodR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RNAmodR' version '1.2.3'
* package encoding: UTF-8
* 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 whether package 'RNAmodR' can be installed ... OK
* 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 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 ... NOTE
Unexported objects imported by ':::' calls:
'BiocGenerics:::replaceSlots' 'Biostrings:::XString'
'IRanges:::.valid.CompressedList' 'IRanges:::coerceToCompressedList'
'S4Vectors:::.valid.DataFrame' 'S4Vectors:::labeledLine'
'S4Vectors:::make_zero_col_DataFrame'
'S4Vectors:::prepare_objects_to_bind'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'.get_inosine_score'
* 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
stats 47.42 2.29 125.95
CoverageSequenceData-class 19.56 3.75 24.42
ModInosine 14.38 0.59 15.69
ProtectedEndSequenceData-class 13.78 0.59 14.92
EndSequenceData-class 12.80 0.51 13.87
PileupSequenceData-class 11.24 0.50 12.58
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
stats 51.14 2.47 122.86
CoverageSequenceData-class 19.21 1.68 21.83
ModInosine 13.97 0.50 15.18
EndSequenceData-class 12.78 0.37 13.72
ProtectedEndSequenceData-class 11.78 0.50 12.95
PileupSequenceData-class 11.03 0.40 12.09
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/RNAmodR.Rcheck/00check.log'
for details.
RNAmodR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/RNAmodR_1.2.3.tar.gz && rm -rf RNAmodR.buildbin-libdir && mkdir RNAmodR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RNAmodR.buildbin-libdir RNAmodR_1.2.3.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL RNAmodR_1.2.3.zip && rm RNAmodR_1.2.3.tar.gz RNAmodR_1.2.3.zip
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% 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 546k 100 546k 0 0 7515k 0 --:--:-- --:--:-- --:--:-- 8283k
install for i386
* installing *source* package 'RNAmodR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RNAmodR'
finding HTML links ... done
CoverageSequenceData-class html
EndSequenceData-class html
ModInosine-functions html
ModInosine-internals html
ModInosine html
Modifier-class html
Modifier-functions html
ModifierSet-class html
NormEndSequenceData-class html
PileupSequenceData-class html
ProtectedEndSequenceData-class html
RNAmodR-datasets html
RNAmodR-development html
RNAmodR-internals html
RNAmodR html
SequenceData-class html
SequenceData-functions html
SequenceDataFrame-class html
SequenceDataList-class html
SequenceDataSet-class html
SequenceModDNAStringSetTrack-class html
SequenceModRNAStringSetTrack-class html
aggregate html
compareByCoord html
modify html
plotData html
plotROC html
settings html
stats html
subsetByCoord 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 'RNAmodR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RNAmodR' as RNAmodR_1.2.3.zip
* DONE (RNAmodR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'RNAmodR' successfully unpacked and MD5 sums checked
|
RNAmodR.Rcheck/tests_i386/testthat.Rout
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(RNAmodR)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Modstrings
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'RNAmodR'
The following object is masked from 'package:testthat':
compare
>
> test_check("RNAmodR")
Error in (function (x) : attempt to apply non-function
== testthat results ===========================================================
[ OK: 187 | SKIPPED: 9 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
53.87 5.43 63.53
|
RNAmodR.Rcheck/tests_x64/testthat.Rout
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(RNAmodR)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Modstrings
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'RNAmodR'
The following object is masked from 'package:testthat':
compare
>
> test_check("RNAmodR")
Error in (function (x) : attempt to apply non-function
== testthat results ===========================================================
[ OK: 187 | SKIPPED: 9 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
65.32 3.50 73.04
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RNAmodR.Rcheck/examples_i386/RNAmodR-Ex.timings
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RNAmodR.Rcheck/examples_x64/RNAmodR-Ex.timings
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