Robert Castelo
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/qpgraph |
| git_branch: RELEASE_3_13 |
| git_last_commit: 80062b5 |
| git_last_commit_date: 2021-05-19 11:42:31 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:17 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the qpgraph package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qpgraph.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 1473/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qpgraph 2.26.0 (landing page) Robert Castelo
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: qpgraph |
| Version: 2.26.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qpgraph.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings qpgraph_2.26.0.tar.gz |
| StartedAt: 2021-10-15 03:58:27 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 04:04:58 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 391.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: qpgraph.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qpgraph.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings qpgraph_2.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/qpgraph.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 'qpgraph/DESCRIPTION' ... OK * this is package 'qpgraph' version '2.26.0' * 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 ... OK * checking for portable file names ... OK * checking whether package 'qpgraph' 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... WARNING Non-portable flags in variable 'PKG_CFLAGS': -Werror=implicit-function-declaration * 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-3.13-bioc/R/library/qpgraph/libs/i386/qpgraph.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/qpgraph/libs/x64/qpgraph.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) 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 installed files from 'inst/doc' ... OK * 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 '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-3.13-bioc/meat/qpgraph.Rcheck/00check.log' for details.
qpgraph.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/qpgraph_2.26.0.tar.gz && rm -rf qpgraph.buildbin-libdir && mkdir qpgraph.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qpgraph.buildbin-libdir qpgraph_2.26.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL qpgraph_2.26.0.zip && rm qpgraph_2.26.0.tar.gz qpgraph_2.26.0.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
94 1858k 94 1754k 0 0 1969k 0 --:--:-- --:--:-- --:--:-- 1969k
100 1858k 100 1858k 0 0 2002k 0 --:--:-- --:--:-- --:--:-- 2002k
install for i386
* installing *source* package 'qpgraph' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cliquer.c -o cliquer.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c graph.c -o graph.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c qpgraph.c -o qpgraph.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c reorder.c -o reorder.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o qpgraph.dll tmp.def cliquer.o graph.o qpgraph.o reorder.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/qpgraph.buildbin-libdir/00LOCK-qpgraph/00new/qpgraph/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
Creating a generic function for 'det' from package 'Matrix' in package 'qpgraph'
** help
*** installing help indices
converting help for package 'qpgraph'
finding HTML links ... done
EcoliOxygen html
HMgmm-class html
SsdMatrix-class html
UGgmm-class html
eQTLcross-class html
eQTLnetwork-class html
eQTLnetworkEstimate html
eQTLnetworkEstimationParam-class html
filterCollinearities html
graphParam-class html
qpAllCItests html
qpAnyGraph html
qpAvgNrr html
qpBoundary html
qpCItest html
qpClique html
qpCliqueNumber html
qpCov html
qpEdgeNrr html
qpFunctionalCoherence html
qpG2Sigma html
qpGenNrr html
qpGetCliques html
qpGraph-class html
qpGraphDensity html
qpHTF html
qpHist html
qpIPF html
qpImportNrr html
qpK2ParCor html
qpNrr html
qpPAC html
qpPCC html
qpPRscoreThreshold html
qpPathWeight html
qpPlotMap html
qpPlotNetwork html
qpPrecisionRecall html
qpRndGraph html
qpRndWishart html
qpTopPairs html
qpUnifRndAssociation html
qpUpdateCliquesRemoving html
qpgraph-package html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/qpgraph.buildbin-libdir/00LOCK-qpgraph/00new/qpgraph/help/qpgraph.html
** building package indices
** installing vignettes
'eQTLnetworks.Rnw'
'qpTxRegNet.Rnw'
'qpgraphSimulate.Rnw'
** testing if installed package can be loaded from temporary location
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
** testing if installed package can be loaded from final location
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'qpgraph' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cliquer.c -o cliquer.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c graph.c -o graph.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c qpgraph.c -o qpgraph.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c reorder.c -o reorder.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o qpgraph.dll tmp.def cliquer.o graph.o qpgraph.o reorder.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/qpgraph.buildbin-libdir/qpgraph/libs/x64
** testing if installed package can be loaded
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
* MD5 sums
packaged installation of 'qpgraph' as qpgraph_2.26.0.zip
* DONE (qpgraph)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'qpgraph' successfully unpacked and MD5 sums checked
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qpgraph.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.
> BiocGenerics:::testPackage("qpgraph")
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
Using t tests for zero partial regression coefficients.
Using exact likelihood ratio tests.
RUNIT TEST PROTOCOL -- Fri Oct 15 04:04:25 2021
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
qpgraph RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
13.51 1.01 14.51
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qpgraph.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.
> BiocGenerics:::testPackage("qpgraph")
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
Using t tests for zero partial regression coefficients.
Using exact likelihood ratio tests.
RUNIT TEST PROTOCOL -- Fri Oct 15 04:04:40 2021
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
qpgraph RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
13.89 0.45 14.36
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qpgraph.Rcheck/examples_i386/qpgraph-Ex.timings
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qpgraph.Rcheck/examples_x64/qpgraph-Ex.timings
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