Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1552/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PICS 2.50.0 (landing page) Renan Sauteraud
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
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 | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the PICS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PICS.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: PICS |
Version: 2.50.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PICS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PICS_2.50.0.tar.gz |
StartedAt: 2024-11-09 09:45:07 -0500 (Sat, 09 Nov 2024) |
EndedAt: 2024-11-09 09:49:51 -0500 (Sat, 09 Nov 2024) |
EllapsedTime: 283.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: PICS.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PICS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PICS_2.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PICS.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PICS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PICS’ version ‘2.50.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 for sufficient/correct file permissions ... OK * checking whether package ‘PICS’ can be installed ... WARNING Found the following significant warnings: pics.c:1963:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] segment.c:123:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/PICS.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... 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 line endings in shell scripts ... 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 compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/PICS/libs/PICS.so’: Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (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 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: 1 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/PICS.Rcheck/00check.log’ for details.
PICS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PICS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘PICS’ ... ** using staged installation checking for pkg-config... /opt/R/arm64/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for GSL... yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pics.c -o pics.o pics.c:1009:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable] double chiSum, etaF, etaR, dd, cc; ^ pics.c:1301:3: warning: variable 'penalty' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ pics.c:1307:97: note: uninitialized use occurs here bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty; ^~~~~~~ pics.c:1275:42: note: initialize the variable 'penalty' to silence this warning double bic, tmp, muF[K], muR[K], penalty, distance; ^ = 0.0 pics.c:1633:69: warning: unused variable 'PhiFw' [-Wunused-variable] double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; ^ pics.c:1633:76: warning: unused variable 'PhiRw' [-Wunused-variable] double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; ^ pics.c:1963:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] if((gsl_matrix_get(Index,kMerge,k)==1) | (gsl_matrix_get(Index,kMerge+1,k)==1)) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ || pics.c:1963:10: note: cast one or both operands to int to silence this warning pics.c:1889:7: warning: unused variable 'i' [-Wunused-variable] int i=0,j=0,k=0,l=0,kMerge=0,flag=0; ^ pics.c:1889:11: warning: unused variable 'j' [-Wunused-variable] int i=0,j=0,k=0,l=0,kMerge=0,flag=0; ^ 7 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c segment.c -o segment.o segment.c:123:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if((length(contF)>0) & (length(contR)>0)) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && segment.c:123:6: note: cast one or both operands to int to silence this warning segment.c:406:6: warning: variable 'pp' is incremented both in the loop header and in the loop body [-Wfor-loop-analysis] pp++; ^ segment.c:395:27: note: incremented here for (pp=start; pp<=p; pp++) { ^ segment.c:536:6: warning: variable 'pp' is incremented both in the loop header and in the loop body [-Wfor-loop-analysis] pp++; ^ segment.c:525:27: note: incremented here for (pp=start; pp<=p; pp++) { ^ segment.c:1489:11: warning: unused variable 'muFilter' [-Wunused-variable] double *muFilter, *deltaFilter, *sFFilter, *sRFilter, *seFilter, *seFilterF, *seFilterR, *scoreFilter, *score; ^ segment.c:1490:8: warning: unused variable 'filter1' [-Wunused-variable] SEXP filter1; ^ segment.c:1494:19: warning: variable 'chr' set but not used [-Wunused-but-set-variable] SEXP ans, x, y, chr, names; ^ 6 warnings generated. clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o PICS.so pics.o segment.o -L/opt/R/arm64/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-PICS/00new/PICS/libs ** 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 ** 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 (PICS)
PICS.Rcheck/PICS-Ex.timings
name | user | system | elapsed | |
segmentPICS | 0.353 | 0.006 | 0.361 | |
setParaPrior | 0.000 | 0.001 | 0.001 | |