Jitao David Zhang
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/BioQC |
| Branch: RELEASE_3_11 |
| Last Commit: e9a8893 |
| Last Changed Date: 2020-04-27 14:53:01 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:10 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE BioQC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 179/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BioQC 1.16.0 Jitao David Zhang
| 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: BioQC |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings BioQC_1.16.0.tar.gz |
| StartedAt: 2020-10-17 02:00:32 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 02:04:25 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 233.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BioQC.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings BioQC_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/BioQC.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 'BioQC/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'BioQC' version '1.16.0' * 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 'BioQC' 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 ... 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... 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-3.11-bioc/R/library/BioQC/libs/i386/BioQC.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BioQC/libs/x64/BioQC.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 ** 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 NOTE See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/BioQC.Rcheck/00check.log' for details.
BioQC.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/BioQC_1.16.0.tar.gz && rm -rf BioQC.buildbin-libdir && mkdir BioQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioQC.buildbin-libdir BioQC_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL BioQC_1.16.0.zip && rm BioQC_1.16.0.tar.gz BioQC_1.16.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
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install for i386
* installing *source* package 'BioQC' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gini.c -o gini.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_gmt.cpp -o read_gmt.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stat_rank.c -o stat_rank.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c wmw_test.c -o wmw_test.o
wmw_test.c: In function 'wmw_test_list':
wmw_test.c:105: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
wmw_test.c: In function 'wmw_test':
wmw_test.c:155: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
wmw_test.c: In function 'signed_wmw_test_list':
wmw_test.c:188: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
wmw_test.c: In function 'signed_wmw_test':
wmw_test.c:257: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o BioQC.dll tmp.def gini.o init.o read_gmt.o stat_rank.o wmw_test.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/BioQC.buildbin-libdir/00LOCK-BioQC/00new/BioQC/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'BioQC'
finding HTML links ... done
BaseIndexList-class html
GmtList-class html
GmtList html
IndexList-class html
IndexList html
SignedGenesets-class html
SignedGenesets html
SignedIndexList-class html
SignedIndexList html
absLog10p html
appendGmtList html
as.GmtList html
entropy html
entropyDiversity html
entropySpecificity html
filterBySize html
filterPmat html
gini html
gmtlist2signedGenesets html
gsDesc html
gsGeneCount html
gsGenes html
gsName html
gsNamespace html
hasNamespace html
isValidBaseIndexList html
isValidGmtList html
isValidIndexList html
isValidSignedGenesets html
isValidSignedIndexList html
matchGenes html
offset-set html
offset html
readGmt html
readSignedGmt html
sampleSpecialization html
setDescAsNamespace html
setGsNamespace html
setNamespace html
show-GmtList-method html
show-IndexList-method html
show-SignedGenesets-method html
show-SignedIndexList-method html
simplifyMatrix html
sub-.GmtList html
sub-sub-.GmtList html
uniqGenesetsByNamespace html
valTypes html
wmwTest html
wmwTestInR 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 'BioQC' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gini.c -o gini.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_gmt.cpp -o read_gmt.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stat_rank.c -o stat_rank.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c wmw_test.c -o wmw_test.o
wmw_test.c: In function 'wmw_test_list':
wmw_test.c:105: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
wmw_test.c: In function 'wmw_test':
wmw_test.c:155: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
wmw_test.c: In function 'signed_wmw_test_list':
wmw_test.c:188: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
wmw_test.c: In function 'signed_wmw_test':
wmw_test.c:257: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o BioQC.dll tmp.def gini.o init.o read_gmt.o stat_rank.o wmw_test.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/BioQC.buildbin-libdir/BioQC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioQC' as BioQC_1.16.0.zip
* DONE (BioQC)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'BioQC' successfully unpacked and MD5 sums checked
|
BioQC.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(BioQC)
Loading required package: Biobase
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> test_check("BioQC")
== testthat results ===========================================================
[ OK: 103 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
8.04 0.29 8.34
|
BioQC.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(BioQC)
Loading required package: Biobase
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> test_check("BioQC")
== testthat results ===========================================================
[ OK: 103 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
7.53 0.14 7.65
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BioQC.Rcheck/examples_i386/BioQC-Ex.timings
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BioQC.Rcheck/examples_x64/BioQC-Ex.timings
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