Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 890/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GraphAlignment 1.69.0 (landing page) Joern P. Meier
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the GraphAlignment package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GraphAlignment.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: GraphAlignment |
Version: 1.69.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GraphAlignment.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GraphAlignment_1.69.0.tar.gz |
StartedAt: 2024-08-21 01:27:07 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 01:27:37 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 30.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GraphAlignment.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GraphAlignment.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GraphAlignment_1.69.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GraphAlignment.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'GraphAlignment/DESCRIPTION' ... OK * this is package 'GraphAlignment' version '1.69.0' * 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 'GraphAlignment' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * 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 whether startup messages can be suppressed ... 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 ... NOTE File 'GraphAlignment/R/GraphAlignment.R': .Last.lib calls: library.dynam.unload("GraphAlignment", libpath) Package detach functions should not call 'library.dynam.unload'. See section 'Good practice' in '?.Last.lib'. AlignNetworks: no visible global function definition for 'rnorm' GenerateExample: no visible global function definition for 'runif' GenerateExample: no visible global function definition for 'rnorm' GenerateExample: no visible global function definition for 'pnorm' InitialAlignment: no visible global function definition for 'rnorm' Undefined global functions or variables: pnorm rnorm runif Consider adding importFrom("stats", "pnorm", "rnorm", "runif") to your NAMESPACE file. * 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 x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/GraphAlignment/libs/x64/GraphAlignment.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'putchar', possibly from 'putchar' (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 nor [v]sprintf. 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 sizes of PDF files under 'inst/doc' ... NOTE 'qpdf' made some significant size reductions: compacted 'GraphAlignment.pdf' from 516Kb to 366Kb consider running tools::compactPDF() on these files, or build the source package with --compact-vignettes * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/GraphAlignment.Rcheck/00check.log' for details.
GraphAlignment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GraphAlignment ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'GraphAlignment' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GA_alloc.c -o GA_alloc.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GA_matrix.c -o GA_matrix.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GA_matrix_R.c -o GA_matrix_R.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GA_message.c -o GA_message.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GA_vector.c -o GA_vector.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GA_vector_R.c -o GA_vector_R.o GA_vector_R.c: In function 'GA_clamp_mode_from_R': GA_vector_R.c:139:9: warning: unused variable 'size' [-Wunused-variable] 139 | int size = LENGTH(robj); | ^~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GraphAlignment.c -o GraphAlignment.o GraphAlignment.c: In function 'GA_encode_directed_graph': GraphAlignment.c:138:20: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 138 | if (matrix->elts[i][j] == 1) | ^ GraphAlignment.c:159:20: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 159 | if (matrix->elts[i][j] == 1) | ^ GraphAlignment.c: In function 'GA_directed_mode_from_R': GraphAlignment.c:264:9: warning: unused variable 'size' [-Wunused-variable] 264 | int size = LENGTH(robj); | ^~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c lap.c -o lap.o lap.c: In function 'LAP_lap': lap.c:260:11: warning: 'min' may be used uninitialized [-Wmaybe-uninitialized] 260 | h = assigncost[i][j1] - v[j1] - min; | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ lap.c:65:8: note: 'min' was declared here 65 | cost min, h, umin, usubmin, v2, *d; | ^~~ lap.c:293:19: warning: 'last' may be used uninitialized [-Wmaybe-uninitialized] 293 | for (k = 0; k <= last; k++) | ~~^~~~~~~ lap.c:64:30: note: 'last' was declared here 64 | col j, j1, j2, endofpath, last, low, up, *collist, *matches; | ^~~~ gcc -shared -s -static-libgcc -o GraphAlignment.dll tmp.def GA_alloc.o GA_matrix.o GA_matrix_R.o GA_message.o GA_vector.o GA_vector_R.o GraphAlignment.o lap.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-GraphAlignment/00new/GraphAlignment/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (GraphAlignment)
GraphAlignment.Rcheck/GraphAlignment-Ex.timings
name | user | system | elapsed | |
AlignNetworks | 0.03 | 0.00 | 0.03 | |
AlignedPairs | 0.01 | 0.00 | 0.02 | |
AnalyzeAlignment | 0.01 | 0.00 | 0.02 | |
ComputeLinkParameters | 0.02 | 0.00 | 0.01 | |
ComputeM | 0 | 0 | 0 | |
ComputeNodeParameters | 0.01 | 0.00 | 0.02 | |
ComputeScores | 0.02 | 0.00 | 0.02 | |
CreateScoreMatrix | 0.00 | 0.01 | 0.01 | |
EncodeDirectedGraph | 0 | 0 | 0 | |
GenerateExample | 0.11 | 0.00 | 0.11 | |
GetBinNumber | 0 | 0 | 0 | |
InitialAlignment | 0 | 0 | 0 | |
InvertPermutation | 0 | 0 | 0 | |
LinearAssignment | 0 | 0 | 0 | |
MatrixToBin | 0 | 0 | 0 | |
Permute | 0 | 0 | 0 | |
Trace | 0 | 0 | 0 | |
VectorToBin | 0 | 0 | 0 | |