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 756/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
garfield 1.33.0 (landing page) Valentina Iotchkova
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the garfield package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/garfield.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: garfield |
Version: 1.33.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:garfield.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings garfield_1.33.0.tar.gz |
StartedAt: 2024-08-21 00:57:37 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 00:58:44 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 66.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: garfield.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:garfield.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings garfield_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/garfield.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 'garfield/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'garfield' version '1.33.0' * 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 'garfield' can be installed ... WARNING Found the following significant warnings: garfield_perm.cpp:306:29: warning: format '%s' expects argument of type 'char*', but argument 2 has type 'long int' [-Wformat=] garfield_perm.cpp:306:32: warning: format '%s' expects argument of type 'char*', but argument 3 has type 'int' [-Wformat=] garfield_perm.cpp:306:38: warning: format '%s' expects argument of type 'char*', but argument 4 has type 'double' [-Wformat=] garfield_perm.cpp:306:41: warning: unknown conversion type character '\x09' in format [-Wformat=] garfield_perm.cpp:306:46: warning: format '%s' expects argument of type 'char*', but argument 5 has type 'int' [-Wformat=] garfield_perm.cpp:306:83: warning: format '%s' expects argument of type 'char*', but argument 6 has type 'double' [-Wformat=] garfield_perm.cpp:356:27: warning: format '%s' expects argument of type 'char*', but argument 2 has type 'int' [-Wformat=] garfield_prep.cpp:144:28: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations] garfield_prep.cpp:225:37: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations] garfield_prep.cpp:234:37: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations] garfield_prep.cpp:245:38: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations] garfield_prep.cpp:273:37: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations] See 'F:/biocbuild/bbs-3.20-bioc/meat/garfield.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.2.0' * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 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 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 garfield.plot: no visible global function definition for 'read.table' garfield.plot: no visible global function definition for 'colorRampPalette' garfield.plot: no visible global function definition for 'pdf' garfield.plot: no visible global function definition for 'layout' garfield.plot: no visible global function definition for 'par' garfield.plot: no visible global function definition for 'title' garfield.plot: no visible global function definition for 'legend' garfield.plot: no visible global function definition for 'dev.off' garfield.plot.fnx: no visible global function definition for 'par' garfield.plot.fnx: no visible global function definition for 'polygon' garfield.plot.fnx: no visible global function definition for 'segments' garfield.plot.fnx: no visible global function definition for 'points' garfield.plot.fnx: no visible global function definition for 'lines' garfield.plot.fnx: no visible global function definition for 'median' garfield.plot.fnx: no visible global function definition for 'text' Undefined global functions or variables: colorRampPalette dev.off layout legend lines median par pdf points polygon read.table segments text title Consider adding importFrom("grDevices", "colorRampPalette", "dev.off", "pdf") importFrom("graphics", "layout", "legend", "lines", "par", "points", "polygon", "segments", "text", "title") importFrom("stats", "median") importFrom("utils", "read.table") 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/garfield/libs/x64/garfield.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'rand', possibly from 'rand' (C) Found 'srand', possibly from 'srand' (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' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed garfield.plot 4.94 0.41 15.64 * 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: 1 WARNING, 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/garfield.Rcheck/00check.log' for details.
garfield.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL garfield ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'garfield' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' using C++ compiler: 'G__~1.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 garfield_init.c -o garfield_init.o g++ -std=gnu++17 -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 garfield_perm.cpp -o garfield_perm.o garfield_perm.cpp: In function 'void batchfeep(std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, const std::vector<bin>&, const std::vector<double>&, int, int, bool, int, double, int, std::vector<bool>)': garfield_perm.cpp:306:29: warning: format '%s' expects argument of type 'char*', but argument 2 has type 'long int' [-Wformat=] 306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec ); | ~^ ~~~ | | | | char* long int | %ld garfield_perm.cpp:306:32: warning: format '%s' expects argument of type 'char*', but argument 3 has type 'int' [-Wformat=] 306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec ); | ~^ ~~~~~~ | | | | char* int | %d garfield_perm.cpp:306:38: warning: format '%s' expects argument of type 'char*', but argument 4 has type 'double' [-Wformat=] 306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec ); | ~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | char* double | %f garfield_perm.cpp:306:41: warning: unknown conversion type character '\x09' in format [-Wformat=] 306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec ); | ^~ garfield_perm.cpp:306:46: warning: format '%s' expects argument of type 'char*', but argument 5 has type 'int' [-Wformat=] 306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec ); | ~^ ~~~~~~ | | | | char* int | %d garfield_perm.cpp:306:83: warning: format '%s' expects argument of type 'char*', but argument 6 has type 'double' [-Wformat=] 306 | Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec ); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | char* double | %f garfield_perm.cpp: In function 'int garfield_perm(char**, char**, char**, char**, char**, char**, char**, char**, char**, char**, char**, char**, char**)': garfield_perm.cpp:356:27: warning: format '%s' expects argument of type 'char*', but argument 2 has type 'int' [-Wformat=] 356 | Rprintf("%s",nannot); | ~^ ~~~~~~ | | | | | int | char* | %d g++ -std=gnu++17 -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 garfield_prep.cpp -o garfield_prep.o garfield_prep.cpp:144:28: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations] 144 | struct Enumerator : public iterator<input_iterator_tag, typename Iterator::value_type> { | ^~~~~~~~ In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_algobase.h:65, from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/algorithm:60, from garfield_prep.cpp:19: C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ garfield_prep.cpp:225:37: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations] 225 | struct TagsOutputIterator1 : public iterator<output_iterator_tag,void,void,void,void> { | ^~~~~~~~ C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ garfield_prep.cpp:234:37: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations] 234 | struct TagsOutputIterator2 : public iterator<output_iterator_tag,void,void,void,void> { | ^~~~~~~~ C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ garfield_prep.cpp:245:38: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations] 245 | struct TagRefOutputIterator : public iterator<output_iterator_tag,void,void,void,void> { | ^~~~~~~~ C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ garfield_prep.cpp:273:37: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations] 273 | struct PrintOutputIterator : public iterator<output_iterator_tag,void,void,void,void> { | ^~~~~~~~ C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ g++ -std=gnu++17 -shared -s -static-libgcc -o garfield.dll tmp.def garfield_init.o garfield_perm.o garfield_prep.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-garfield/00new/garfield/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 (garfield)
garfield.Rcheck/garfield-Ex.timings
name | user | system | elapsed | |
garfield.plot | 4.94 | 0.41 | 15.64 | |
garfield.plot.fnx | 0 | 0 | 0 | |
garfield.run | 1.40 | 0.14 | 1.56 | |