Ahmed Mohamed
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/NetPathMiner |
| git_branch: RELEASE_3_19 |
| git_last_commit: 6e1a540 |
| git_last_commit_date: 2024-10-15 10:47:44 -0400 (Tue, 15 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:38 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 1421/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NetPathMiner 1.40.2 (landing page) Ahmed Mohamed
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the NetPathMiner package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NetPathMiner.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: NetPathMiner |
| Version: 1.40.2 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL NetPathMiner |
| StartedAt: 2024-10-16 15:50:49 -0400 (Wed, 16 Oct 2024) |
| EndedAt: 2024-10-16 15:51:05 -0400 (Wed, 16 Oct 2024) |
| EllapsedTime: 16.7 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL NetPathMiner
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘NetPathMiner’ ...
** using staged installation
'config' variable 'CPP' is defunct
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for xmlParseFile in -lxml2... yes
checking for readSBML in -lsbml... yes
libSBML found, finding configuration...
pkg-config tool found
libsbml.pc found. Using pkg-config to extract it.
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c handlesegfault.c -o handlesegfault.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c hme3m.c -o hme3m.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c kgml_interface.cpp -o kgml_interface.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c methods.cpp -o methods.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c sbml_interface.cpp -o sbml_interface.o
sbml_interface.cpp: In function ‘SEXPREC* readsbmlfile(SEXP, SEXP, SEXP)’:
sbml_interface.cpp:44:47: warning: format not a string literal and no format arguments [-Wformat-security]
44 | Rf_warningcall(mkChar(filename), message.str().c_str());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sbml_interface.cpp:48:31: warning: format not a string literal and no format arguments [-Wformat-security]
48 | Rf_warningcall(mkChar(filename), message.str().c_str());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sbml_interface.cpp: In function ‘SEXPREC* readsbml_sign(SEXP, SEXP, SEXP)’:
sbml_interface.cpp:369:39: warning: format not a string literal and no format arguments [-Wformat-security]
369 | Rf_warningcall(mkChar(filename), message.str().c_str());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o NetPathMiner.so handlesegfault.o hme3m.o init.o kgml_interface.o methods.o sbml_interface.o -lsbml -lxml2 -lxml2 -lsbml -llapack -L/home/biocbuild/bbs-3.19-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-NetPathMiner/00new/NetPathMiner/libs
** R
** data
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (NetPathMiner)