| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:03 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the easyRNASeq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/easyRNASeq.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 546/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| easyRNASeq 2.28.0 (landing page) Nicolas Delhomme
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: easyRNASeq |
| Version: 2.28.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:easyRNASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings easyRNASeq_2.28.0.tar.gz |
| StartedAt: 2021-10-14 22:36:47 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 22:55:19 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 1112.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: easyRNASeq.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:easyRNASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings easyRNASeq_2.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/easyRNASeq.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'easyRNASeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'easyRNASeq' version '2.28.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Files named as vignettes but with no recognized vignette engine:
'inst/doc/01-Introduction.Rmd'
'inst/doc/02-AnnotParam.Rmd'
'inst/doc/03-SyntheticTranscripts.Rmd'
'inst/doc/04-BamParam.Rmd'
'inst/doc/05-RnaSeqParam.Rmd'
'inst/doc/06-simpleRNASeq.Rmd'
'inst/doc/07-cleanUp.Rmd'
'inst/doc/08-Session-Info.Rmd'
'inst/doc/09-Acknowledgments.Rmd'
'inst/doc/10-Foonotes.Rmd'
'inst/doc/11-Images.Rmd'
'inst/doc/12-Appendix.Rmd'
(Is a VignetteBuilder field missing?)
* 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 'easyRNASeq' 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
Namespace in Imports field not imported from: 'locfit'
All declared Imports should be used.
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
easyRNASeq-simpleRNASeq 118.02 0.69 121.41
easyRNASeq-package 61.84 5.34 68.34
easyRNASeq-synthetic-transcripts 41.95 0.08 42.12
BiocFileCache-methods 30.42 1.47 46.33
easyRNASeq-BamFileList 13.78 0.58 15.70
Rsamtools-methods 10.85 0.23 12.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
easyRNASeq-simpleRNASeq 92.05 0.91 94.04
easyRNASeq-package 55.31 0.76 57.24
easyRNASeq-synthetic-transcripts 33.86 0.15 34.10
BiocFileCache-methods 21.00 0.61 31.16
easyRNASeq-BamFileList 15.02 0.58 16.92
Rsamtools-methods 11.87 0.40 13.27
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/easyRNASeq.Rcheck/00check.log'
for details.
easyRNASeq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/easyRNASeq_2.28.0.tar.gz && rm -rf easyRNASeq.buildbin-libdir && mkdir easyRNASeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=easyRNASeq.buildbin-libdir easyRNASeq_2.28.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL easyRNASeq_2.28.0.zip && rm easyRNASeq_2.28.0.tar.gz easyRNASeq_2.28.0.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
81 119k 81 99687 0 0 516k 0 --:--:-- --:--:-- --:--:-- 517k
100 119k 100 119k 0 0 632k 0 --:--:-- --:--:-- --:--:-- 633k
install for i386
* installing *source* package 'easyRNASeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'basename' from package 'base' in package 'easyRNASeq'
Creating a generic function for 'file.exists' from package 'base' in package 'easyRNASeq'
** help
*** installing help indices
converting help for package 'easyRNASeq'
finding HTML links ... done
BiocFileCache-methods html
finding level-2 HTML links ... done
GenomicRanges-methods html
IRanges-methods html
Rsamtools-methods html
ShortRead-methods html
basename-methods html
easyRNASeq-AnnotParam-accessors html
easyRNASeq-AnnotParam-class html
easyRNASeq-AnnotParam html
easyRNASeq-BamFileList html
easyRNASeq-BamParam-accessors html
easyRNASeq-BamParam-class html
easyRNASeq-BamParam html
easyRNASeq-RnaSeqParam-accessors html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/easyRNASeq.buildbin-libdir/00LOCK-easyRNASeq/00new/easyRNASeq/help/bamParam.html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/easyRNASeq.buildbin-libdir/00LOCK-easyRNASeq/00new/easyRNASeq/help/annotParam.html
easyRNASeq-RnaSeqParam-class html
easyRNASeq-RnaSeqParam html
easyRNASeq-accessors html
easyRNASeq-annotation-internal-methods
html
easyRNASeq-annotation-methods html
easyRNASeq-class html
easyRNASeq-correction-methods html
easyRNASeq-coverage-methods html
easyRNASeq-datasets html
easyRNASeq-defunct-annotation-methods html
easyRNASeq-defunct html
easyRNASeq-easyRNASeq html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/easyRNASeq.buildbin-libdir/00LOCK-easyRNASeq/00new/easyRNASeq/help/easyRNASeq-defunct.html
easyRNASeq-global-variables html
easyRNASeq-internal-AnnotParam-methods
html
easyRNASeq-internal-methods html
easyRNASeq-island-methods html
easyRNASeq-package html
easyRNASeq-simpleRNASeq html
easyRNASeq-summarization-internal-methods
html
easyRNASeq-summarization-methods html
easyRNASeq-synthetic-transcripts html
edgeR-methods html
file.exists-methods html
genomeIntervals-methods html
parallel-methods html
print-methods html
show-methods 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 'easyRNASeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'easyRNASeq' as easyRNASeq_2.28.0.zip
* DONE (easyRNASeq)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'easyRNASeq' successfully unpacked and MD5 sums checked
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easyRNASeq.Rcheck/tests_i386/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.
> # get the example data
> library(easyRNASeq)
> tutorialData()
[1] "C:/Users/BIOCBU~1/AppData/Local/easyRNASeq/easyRNASeq/Cache"
>
> # set the env.var
> #TUTORIAL.DATA <- get("TUTORIAL.DATA",envir=as.environment("package:easyRNASeq"))
>
> # run the tests
> BiocGenerics:::testPackage("easyRNASeq")
Loading required package: GenomicRanges
Loading required package: stats4
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 object is masked from 'package:easyRNASeq':
basename
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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
No validation performed at that stage
Validated a datasource of type biomaRt
No validation performed at that stage
Validated a datasource of type rda
Read 1000 records
Validated a datasource of type gtf
Read 999 records
Validated a datasource of type gff3
RUNIT TEST PROTOCOL -- Thu Oct 14 22:53:23 2021
***********************************************
Number of test functions: 20
Number of errors: 0
Number of failures: 0
1 Test Suite :
easyRNASeq RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20
Number of errors: 0
Number of failures: 0
Warning messages:
1: In FUN(X[[i]], ...) :
Bam file: 38381211785_ACTAGC.bam is considered unstranded.
2: In FUN(X[[i]], ...) :
Bam file: 38381211785_ACTAGC.bam Strandedness could not be determined using 14772 regions spanning 1023473 bp on either strand at a 90% cutoff; 76.6 percent appear to be stranded.
3: In FUN(X[[i]], ...) :
Bam file: 38384ca754a_TTGCGA.bam is considered unstranded.
4: In FUN(X[[i]], ...) :
Bam file: 38384ca754a_TTGCGA.bam Strandedness could not be determined using 19659 regions spanning 1381886 bp on either strand at a 90% cutoff; 73.37 percent appear to be stranded.
5: In FUN(X[[i]], ...) :
Bam file: 3838662850b9_ATGGCT.bam is considered unstranded.
6: In FUN(X[[i]], ...) :
Bam file: 3838662850b9_ATGGCT.bam Strandedness could not be determined using 18462 regions spanning 1280337 bp on either strand at a 90% cutoff; 74.26 percent appear to be stranded.
7: In FUN(X[[i]], ...) :
Bam file: 3838738db96_ACACTG.bam is considered unstranded.
8: In FUN(X[[i]], ...) :
Bam file: 3838738db96_ACACTG.bam Strandedness could not be determined using 18615 regions spanning 1300192 bp on either strand at a 90% cutoff; 73.67 percent appear to be stranded.
9: In simpleRNASeq(bamFiles = bamFiles, param = param, verbose = FALSE) :
As of version 2.15.5, easyRNASeq assumes that, if the data is strand specific, the sequencing was done using a protocol such as the Illumina TruSeq, where the reverse strand is quantified - i.e. the strandProtocol argument of the BamParam class defaults to 'reverse'.
>
> # cleanup
> # removebfc(easyRNASeq:::.get_cache(),ask=FALSE)
>
> proc.time()
user system elapsed
101.10 3.79 116.06
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easyRNASeq.Rcheck/tests_x64/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.
> # get the example data
> library(easyRNASeq)
> tutorialData()
[1] "C:/Users/BIOCBU~1/AppData/Local/easyRNASeq/easyRNASeq/Cache"
>
> # set the env.var
> #TUTORIAL.DATA <- get("TUTORIAL.DATA",envir=as.environment("package:easyRNASeq"))
>
> # run the tests
> BiocGenerics:::testPackage("easyRNASeq")
Loading required package: GenomicRanges
Loading required package: stats4
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 object is masked from 'package:easyRNASeq':
basename
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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
No validation performed at that stage
Validated a datasource of type biomaRt
No validation performed at that stage
Validated a datasource of type rda
Read 1000 records
Validated a datasource of type gtf
Read 999 records
Validated a datasource of type gff3
RUNIT TEST PROTOCOL -- Thu Oct 14 22:55:10 2021
***********************************************
Number of test functions: 20
Number of errors: 0
Number of failures: 0
1 Test Suite :
easyRNASeq RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20
Number of errors: 0
Number of failures: 0
Warning messages:
1: In FUN(X[[i]], ...) :
Bam file: 38381211785_ACTAGC.bam is considered unstranded.
2: In FUN(X[[i]], ...) :
Bam file: 38381211785_ACTAGC.bam Strandedness could not be determined using 14772 regions spanning 1023473 bp on either strand at a 90% cutoff; 76.6 percent appear to be stranded.
3: In FUN(X[[i]], ...) :
Bam file: 38384ca754a_TTGCGA.bam is considered unstranded.
4: In FUN(X[[i]], ...) :
Bam file: 38384ca754a_TTGCGA.bam Strandedness could not be determined using 19659 regions spanning 1381886 bp on either strand at a 90% cutoff; 73.37 percent appear to be stranded.
5: In FUN(X[[i]], ...) :
Bam file: 3838662850b9_ATGGCT.bam is considered unstranded.
6: In FUN(X[[i]], ...) :
Bam file: 3838662850b9_ATGGCT.bam Strandedness could not be determined using 18462 regions spanning 1280337 bp on either strand at a 90% cutoff; 74.26 percent appear to be stranded.
7: In FUN(X[[i]], ...) :
Bam file: 3838738db96_ACACTG.bam is considered unstranded.
8: In FUN(X[[i]], ...) :
Bam file: 3838738db96_ACACTG.bam Strandedness could not be determined using 18615 regions spanning 1300192 bp on either strand at a 90% cutoff; 73.67 percent appear to be stranded.
9: In simpleRNASeq(bamFiles = bamFiles, param = param, verbose = FALSE) :
As of version 2.15.5, easyRNASeq assumes that, if the data is strand specific, the sequencing was done using a protocol such as the Illumina TruSeq, where the reverse strand is quantified - i.e. the strandProtocol argument of the BamParam class defaults to 'reverse'.
>
> # cleanup
> # removebfc(easyRNASeq:::.get_cache(),ask=FALSE)
>
> proc.time()
user system elapsed
94.67 2.07 106.32
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easyRNASeq.Rcheck/examples_i386/easyRNASeq-Ex.timings
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easyRNASeq.Rcheck/examples_x64/easyRNASeq-Ex.timings
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