Nicolas Delhomme
| Snapshot Date: 2019-04-01 17:01:18 -0400 (Mon, 01 Apr 2019) |
| URL: https://git.bioconductor.org/packages/easyRNASeq |
| Branch: RELEASE_3_8 |
| Last Commit: eae6fe0 |
| Last Changed Date: 2019-01-04 13:05:21 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-02 11:36:56 -0400 (Tue, 02 Apr 2019).
| Package 447/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| easyRNASeq 2.18.3 Nicolas Delhomme
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | ERROR | skipped | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped |
| Package: easyRNASeq |
| Version: 2.18.3 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:easyRNASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings easyRNASeq_2.18.3.tar.gz |
| StartedAt: 2019-04-02 01:45:01 -0400 (Tue, 02 Apr 2019) |
| EndedAt: 2019-04-02 01:58:56 -0400 (Tue, 02 Apr 2019) |
| EllapsedTime: 835.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: easyRNASeq.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:easyRNASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings easyRNASeq_2.18.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/easyRNASeq.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '2.18.3'
* 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/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 ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpumCvGh/R.INSTALL1fa460561a25/easyRNASeq/man/easyRNASeq-annotation-methods.Rd:38: file link 'readGff3' in package 'genomeIntervals' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpumCvGh/R.INSTALL1fa460561a25/easyRNASeq/man/easyRNASeq-package.Rd:133: file link 'BamFileList-class' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpumCvGh/R.INSTALL1fa460561a25/easyRNASeq/man/genomeIntervals-methods.Rd:39: file link 'readGff3' in package 'genomeIntervals' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/easyRNASeq.Rcheck/00install.out' for details.
* 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 ... 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 ... 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 or elapsed time > 5s
user system elapsed
easyRNASeq-simpleRNASeq 76.38 0.74 78.23
easyRNASeq-package 53.28 7.20 61.58
easyRNASeq-synthetic-transcripts 46.64 0.81 47.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
easyRNASeq-simpleRNASeq 69.11 0.57 70.11
easyRNASeq-package 47.01 1.18 49.00
easyRNASeq-synthetic-transcripts 41.35 0.46 42.39
* 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: 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/easyRNASeq.Rcheck/00check.log'
for details.
easyRNASeq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/easyRNASeq_2.18.3.tar.gz && rm -rf easyRNASeq.buildbin-libdir && mkdir easyRNASeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=easyRNASeq.buildbin-libdir easyRNASeq_2.18.3.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL easyRNASeq_2.18.3.zip && rm easyRNASeq_2.18.3.tar.gz easyRNASeq_2.18.3.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 121k 100 121k 0 0 1410k 0 --:--:-- --:--:-- --:--:-- 1479k
install for i386
* installing *source* package 'easyRNASeq' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'IRanges' for request: 'rev' when loading 'easyRNASeq'
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
DESeq-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
easyRNASeq-RnaSeqParam-class html
easyRNASeq-RnaSeqParam html
easyRNASeq-accessors html
easyRNASeq-annotation-internal-methods
html
easyRNASeq-annotation-methods html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpumCvGh/R.INSTALL1fa460561a25/easyRNASeq/man/easyRNASeq-annotation-methods.Rd:38: file link 'readGff3' in package 'genomeIntervals' does not exist and so has been treated as a topic
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
easyRNASeq-global-variables html
easyRNASeq-internal-AnnotParam-methods
html
easyRNASeq-internal-methods html
easyRNASeq-island-methods html
easyRNASeq-package html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpumCvGh/R.INSTALL1fa460561a25/easyRNASeq/man/easyRNASeq-package.Rd:133: file link 'BamFileList-class' in package 'Rsamtools' does not exist and so has been treated as a topic
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
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpumCvGh/R.INSTALL1fa460561a25/easyRNASeq/man/genomeIntervals-methods.Rd:39: file link 'readGff3' in package 'genomeIntervals' does not exist and so has been treated as a topic
parallel-methods html
print-methods html
show-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'rev' when loading 'easyRNASeq'
In R CMD INSTALL
install for x64
* installing *source* package 'easyRNASeq' ...
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'rev' when loading 'easyRNASeq'
* MD5 sums
packaged installation of 'easyRNASeq' as easyRNASeq_2.18.3.zip
* DONE (easyRNASeq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'easyRNASeq' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
easyRNASeq.Rcheck/tests_i386/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 and annotation files from GitHub using curl
> library(curl)
> exFiles <- c("gAnnot.rda",
+ "Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz",
+ "Dmel-mRNA-exon-r5.52.gff3.gz",
+ "ACACTG.bam","ACTAGC.bam","ATGGCT.bam","TTGCGA.bam",
+ "ACACTG.bam.bai","ACTAGC.bam.bai","ATGGCT.bam.bai","TTGCGA.bam.bai")
>
> invisible(sapply(exFiles,function(f){
+ if(!file.exists(f)){
+ invisible(curl_download(paste0("https://github.com/UPSCb/UPSCb/raw/",
+ "master/tutorial/easyRNASeq/",f),f))
+ }
+ }))
>
> # run the tests
> BiocGenerics:::testPackage("easyRNASeq")
No methods found in package 'IRanges' for request: 'rev' when loading '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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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 -- Tue Apr 02 01:57:41 2019
***********************************************
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
There were 11 warnings (use warnings() to see them)
>
> # cleanup
> file.remove(exFiles)
[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
>
> proc.time()
user system elapsed
49.87 1.82 87.09
|
easyRNASeq.Rcheck/tests_x64/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 and annotation files from GitHub using curl
> library(curl)
> exFiles <- c("gAnnot.rda",
+ "Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz",
+ "Dmel-mRNA-exon-r5.52.gff3.gz",
+ "ACACTG.bam","ACTAGC.bam","ATGGCT.bam","TTGCGA.bam",
+ "ACACTG.bam.bai","ACTAGC.bam.bai","ATGGCT.bam.bai","TTGCGA.bam.bai")
>
> invisible(sapply(exFiles,function(f){
+ if(!file.exists(f)){
+ invisible(curl_download(paste0("https://github.com/UPSCb/UPSCb/raw/",
+ "master/tutorial/easyRNASeq/",f),f))
+ }
+ }))
>
> # run the tests
> BiocGenerics:::testPackage("easyRNASeq")
No methods found in package 'IRanges' for request: 'rev' when loading '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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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 -- Tue Apr 02 01:58:50 2019
***********************************************
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
There were 11 warnings (use warnings() to see them)
>
> # cleanup
> file.remove(exFiles)
[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
>
> proc.time()
user system elapsed
44.00 0.98 68.73
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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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