Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
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 | |||||||||
nebbiolo2 | 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 | |||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: PICS |
Version: 2.50.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:PICS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PICS_2.50.0.tar.gz |
StartedAt: 2024-11-20 11:00:55 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 11:04:46 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 230.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PICS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:PICS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PICS_2.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/PICS.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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 ... 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 ... OK * used C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ * 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 loading without being on the library search path ... 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 * 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 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/PICS.Rcheck/00check.log’ for details.
PICS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL PICS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘PICS’ ... ** using staged installation checking for pkg-config... /usr/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: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c pics.c -o pics.o pics.c: In function 'ECM2': pics.c:1009:16: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable] 1009 | double chiSum, etaF, etaR, dd, cc; | ^~~~~~ pics.c: In function 'getInfMat': pics.c:1633:83: warning: unused variable 'PhiRw' [-Wunused-variable] 1633 | double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; | ^~~~~ pics.c:1633:76: warning: unused variable 'PhiFw' [-Wunused-variable] 1633 | double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; | ^~~~~ pics.c: In function 'mergePeak': pics.c:1889:11: warning: unused variable 'j' [-Wunused-variable] 1889 | int i=0,j=0,k=0,l=0,kMerge=0,flag=0; | ^ pics.c:1889:7: warning: unused variable 'i' [-Wunused-variable] 1889 | int i=0,j=0,k=0,l=0,kMerge=0,flag=0; | ^ pics.c: In function 'BIC': pics.c:1307:13: warning: 'penalty' may be used uninitialized [-Wmaybe-uninitialized] 1307 | bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty; | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pics.c:1275:42: note: 'penalty' was declared here 1275 | double bic, tmp, muF[K], muR[K], penalty, distance; | ^~~~~~~ pics.c: In function 'fitModelK': pics.c:494:23: warning: 'firstFit' may be used uninitialized [-Wmaybe-uninitialized] 494 | return(ans); | ^ pics.c:421:25: note: 'firstFit' was declared here 421 | SEXP ans, temp, firstFit; | ^~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c segment.c -o segment.o segment.c: In function 'getDensity': segment.c:1494:19: warning: variable 'chr' set but not used [-Wunused-but-set-variable] 1494 | SEXP ans, x, y, chr, names; | ^~~ segment.c:1490:8: warning: unused variable 'filter1' [-Wunused-variable] 1490 | SEXP filter1; | ^~~~~~~ segment.c:1489:11: warning: unused variable 'muFilter' [-Wunused-variable] 1489 | double *muFilter, *deltaFilter, *sFFilter, *sRFilter, *seFilter, *seFilterF, *seFilterR, *scoreFilter, *score; | ^~~~~~~~ gcc -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o PICS.so pics.o segment.o -lgsl -lgslcblas -lm -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-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 | 1.303 | 0.060 | 1.369 | |
setParaPrior | 0.001 | 0.000 | 0.002 | |