Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1564/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
plier 1.76.0 (landing page) Crispin Miller
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the plier package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/plier.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: plier |
Version: 1.76.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL plier |
StartedAt: 2024-12-19 15:05:57 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 15:06:04 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 6.5 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL plier ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘plier’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c affyplier.cpp -o affyplier.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c plier_impl.cpp -o plier_impl.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c plieralg.cpp -o plieralg.o plieralg.cpp: In function ‘long int NewtonPlier(plier_data*, double&)’: plieralg.cpp:905:21: warning: variable ‘icount’ set but not used [-Wunused-but-set-variable] 905 | long count, icount; | ^~~~~~ plieralg.cpp: At global scope: plieralg.cpp:49:12: warning: ‘g_ErrorCode’ defined but not used [-Wunused-variable] 49 | static int g_ErrorCode=NoError; | ^~~~~~~~~~~ plieralg.cpp: In function ‘long int NewtonPlier(plier_data*, double&)’: plieralg.cpp:1257:31: warning: ‘LogLikelihood’ may be used uninitialized [-Wmaybe-uninitialized] 1257 | output = LogLikelihood/nSize; | ~~~~~~~~~~~~~^~~~~~ plieralg.cpp:910:16: note: ‘LogLikelihood’ was declared here 910 | double LogLikelihood; | ^~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rwrapper.cpp -o rwrapper.o rwrapper.cpp: In function ‘void one_probeset(bool*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, int*, bool*, bool*, bool*, double*, double*, int*, int*, int*, long int*, double*, double*, double*, double*, int*)’: rwrapper.cpp:192:12: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 192 | delete pm_ptr; | ^~~~~~ rwrapper.cpp:151:44: note: returned from ‘void* operator new [](std::size_t)’ 151 | double **pm_ptr = new double *[*num_exp]; | ^ rwrapper.cpp:193:12: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 193 | delete mm_ptr; | ^~~~~~ rwrapper.cpp:152:44: note: returned from ‘void* operator new [](std::size_t)’ 152 | double **mm_ptr = new double *[*num_exp]; | ^ rwrapper.cpp:194:12: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 194 | delete rpct; | ^~~~ rwrapper.cpp:159:39: note: returned from ‘void* operator new [](std::size_t)’ 159 | long *rpct = new long [*num_exp]; /* the API expects a long array that it wants to delete itself (replicate). We have an int array that R owns so we need to create the long one here, but let the API handle the clean up. Which is nice. */ | ^ g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o plier.so affyplier.o plier_impl.o plieralg.o rwrapper.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-plier/00new/plier/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (plier)