Welliton Souza
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/Rqc |
| Branch: RELEASE_3_7 |
| Last Commit: 029044f |
| Last Changed Date: 2018-04-30 10:35:35 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:39:37 -0400 (Wed, 17 Oct 2018).
| Package 1276/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rqc 1.14.0 Welliton Souza
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Rqc |
| Version: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rqc.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Rqc_1.14.0.tar.gz |
| StartedAt: 2018-10-17 04:33:08 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 04:41:27 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 499.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Rqc.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rqc.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Rqc_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Rqc.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rqc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rqc' version '1.14.0'
* 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:
.travis.yml
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 'Rqc' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAl9IxC/R.INSTALL26d84ef61286/Rqc/man/rqcQA.Rd:65: file link 'FastqFile' in package 'ShortRead' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAl9IxC/R.INSTALL26d84ef61286/Rqc/man/rqcQA.Rd:66: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Rqc.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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rqc/libs/i386/Rqc.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Rqc-package 13.48 1.48 15.39
rqcReport 12.08 0.49 12.64
rqc 11.12 0.55 11.81
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Rqc-package 12.64 0.56 13.39
rqc 12.17 0.50 12.78
rqcReport 11.47 0.39 11.95
* 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, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/Rqc.Rcheck/00check.log'
for details.
Rqc.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/Rqc_1.14.0.tar.gz && rm -rf Rqc.buildbin-libdir && mkdir Rqc.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rqc.buildbin-libdir Rqc_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Rqc_1.14.0.zip && rm Rqc_1.14.0.tar.gz Rqc_1.14.0.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
100 56315 100 56315 0 0 984k 0 --:--:-- --:--:-- --:--:-- 1122k
install for i386
* installing *source* package 'Rqc' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RRDNA.cpp -o RRDNA.o
RRDNA.cpp: In function 'Rcpp::StringVector toRRDNA(Rcpp::StringVector)':
RRDNA.cpp:51:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j = 0; j < dna.size(); j+=3)
^
RRDNA.cpp: In function 'Rcpp::StringVector fromRRDNA(Rcpp::StringVector)':
RRDNA.cpp:102:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(j = 1; j < rrdna.size(); ++j) {
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Rqc.dll tmp.def RRDNA.o RcppExports.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Rqc.buildbin-libdir/Rqc/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Rqc'
finding HTML links ... done
Rqc-package html
RqcResultSet-class html
checkpoint html
detectFileFormat html
fromRRDNA html
matdist html
rqc html
finding level-2 HTML links ... done
rqcCycleAverageQualityPcaPlot html
rqcCycleAverageQualityPlot html
rqcCycleBaseCallsPlot html
rqcCycleGCPlot html
rqcCycleQualityBoxPlot html
rqcCycleQualityPlot html
rqcFileHeatmap html
rqcGroupCycleAverageQualityPlot html
rqcQA html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAl9IxC/R.INSTALL26d84ef61286/Rqc/man/rqcQA.Rd:65: file link 'FastqFile' in package 'ShortRead' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAl9IxC/R.INSTALL26d84ef61286/Rqc/man/rqcQA.Rd:66: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
rqcReadFrequencyPlot html
rqcReadQualityBoxPlot html
rqcReadQualityPlot html
rqcReadWidthPlot html
rqcReport html
rqcShinyReport html
stats4trim html
subsetByGroup html
subsetByPair html
toRRDNA html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'Rqc' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RRDNA.cpp -o RRDNA.o
RRDNA.cpp: In function 'Rcpp::StringVector toRRDNA(Rcpp::StringVector)':
RRDNA.cpp:51:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j = 0; j < dna.size(); j+=3)
^
RRDNA.cpp: In function 'Rcpp::StringVector fromRRDNA(Rcpp::StringVector)':
RRDNA.cpp:102:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(j = 1; j < rrdna.size(); ++j) {
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Rqc.dll tmp.def RRDNA.o RcppExports.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Rqc.buildbin-libdir/Rqc/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rqc' as Rqc_1.14.0.zip
* DONE (Rqc)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'Rqc' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
Rqc.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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(Rqc)
Loading required package: BiocParallel
Loading required package: ShortRead
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, 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: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
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: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:Biostrings':
type
The following objects are masked from 'package:base':
aperm, apply
Loading required package: ggplot2
>
> test_check("Rqc")
== testthat results ===========================================================
OK: 27 SKIPPED: 0 FAILED: 0
Warning messages:
1: In if (is.null(value)) { :
closing unused connection 5 (C:/Users/biocbuild/bbs-3.7-bioc/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz)
2: In if (is.null(value)) { :
closing unused connection 4 (C:/Users/biocbuild/bbs-3.7-bioc/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz)
>
> proc.time()
user system elapsed
15.32 1.90 17.21
|
Rqc.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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(Rqc)
Loading required package: BiocParallel
Loading required package: ShortRead
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, 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: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
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: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:Biostrings':
type
The following objects are masked from 'package:base':
aperm, apply
Loading required package: ggplot2
>
> test_check("Rqc")
== testthat results ===========================================================
OK: 27 SKIPPED: 0 FAILED: 0
Warning messages:
1: In sys.parent() :
closing unused connection 5 (C:/Users/biocbuild/bbs-3.7-bioc/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz)
2: In sys.parent() :
closing unused connection 4 (C:/Users/biocbuild/bbs-3.7-bioc/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz)
>
> proc.time()
user system elapsed
19.37 1.64 21.00
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Rqc.Rcheck/examples_i386/Rqc-Ex.timings
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Rqc.Rcheck/examples_x64/Rqc-Ex.timings
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