Bioconductor Package Maintainer
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/graph |
| Branch: RELEASE_3_12 |
| Last Commit: 03ad9ed |
| Last Changed Date: 2020-10-27 10:22:18 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:31:39 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the graph package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 780/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graph 1.68.0 (landing page) Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: graph |
| Version: 1.68.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:graph.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings graph_1.68.0.tar.gz |
| StartedAt: 2021-05-06 03:23:31 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:24:58 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 86.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graph.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:graph.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings graph_1.68.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/graph.Rcheck' * using R version 4.0.5 (2021-03-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'graph/DESCRIPTION' ... OK * this is package 'graph' version '1.68.0' * 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 'graph' 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 'library' or 'require' call to 'package' in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * 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 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 include directives 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-3.12-bioc/R/library/graph/libs/i386/BioC_graph.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/graph/libs/x64/BioC_graph.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 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 'graph_unit_tests.R' OK ** running tests for arch 'x64' ... Running 'graph_unit_tests.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-3.12-bioc/meat/graph.Rcheck/00check.log' for details.
graph.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/graph_1.68.0.tar.gz && rm -rf graph.buildbin-libdir && mkdir graph.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=graph.buildbin-libdir graph_1.68.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL graph_1.68.0.zip && rm graph_1.68.0.tar.gz graph_1.68.0.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
3 326k 3 11437 0 0 27254 0 0:00:12 --:--:-- 0:00:12 27230
100 326k 100 326k 0 0 772k 0 --:--:-- --:--:-- --:--:-- 771k
install for i386
* installing *source* package 'graph' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/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 -shared -s -static-libgcc -o graph.dll tmp.def graph.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
mv graph.dll BioC_graph.dll
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/graph.buildbin-libdir/00LOCK-graph/00new/graph/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'graph'
finding HTML links ... done
DFS html
IMCA html
MAPKsig html
MultiGraph-class html
acc-methods html
addEdge html
addNode html
adj-methods html
adjacencyMatrix html
apoptosisGraph html
attrData-class html
attrDataItem-methods html
attrDefaults-methods html
aveNumEdges html
biocRepos html
boundary html
calcProb html
calcSumProb html
clearNode html
clusterGraph-class html
clusteringCoefficient-methods html
combineNodes html
defunct html
distGraph-class html
duplicatedEdges html
edgeData-methods html
edgeDataDefaults-methods html
edgeMatrix html
edgeSets html
edgeWeights html
fromGXL-methods html
graph-class html
graph2SparseM html
graphAM-class html
graphBAM-class html
graphExamples html
graphNEL-class html
inEdges html
internal html
isAdjacent-methods html
isDirected-methods html
leaves html
listEdges html
matrix2Graph html
mostEdges html
multigraph html
nodeData-methods html
nodeDataDefaults-methods html
numNoEdges html
pancrCaIni html
randomEGraph html
randomGraph html
randomNodeGraph html
removeEdge html
removeNode html
renderInfo-class html
reverseEdgeDirections html
settings html
simpleEdge-class html
standardLabeling html
subGraph html
toDotR-methods html
toDotWithRI html
ugraph html
validGraph html
write.tlp 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 'graph' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/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 -shared -s -static-libgcc -o graph.dll tmp.def graph.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
mv graph.dll BioC_graph.dll
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/graph.buildbin-libdir/graph/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'graph' as graph_1.68.0.zip
* DONE (graph)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'graph' successfully unpacked and MD5 sums checked
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graph.Rcheck/tests_i386/graph_unit_tests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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("graph", pattern="_test.R")
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.max, which.min
RUNIT TEST PROTOCOL -- Thu May 06 03:24:44 2021
***********************************************
Number of test functions: 206
Number of errors: 0
Number of failures: 0
1 Test Suite :
graph RUnit Tests - 206 test functions, 0 errors, 0 failures
Number of test functions: 206
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
5.73 0.12 5.84
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graph.Rcheck/tests_x64/graph_unit_tests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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("graph", pattern="_test.R")
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.max, which.min
RUNIT TEST PROTOCOL -- Thu May 06 03:24:49 2021
***********************************************
Number of test functions: 206
Number of errors: 0
Number of failures: 0
1 Test Suite :
graph RUnit Tests - 206 test functions, 0 errors, 0 failures
Number of test functions: 206
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
4.84 0.10 4.93
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graph.Rcheck/examples_i386/graph-Ex.timings
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graph.Rcheck/examples_x64/graph-Ex.timings
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