Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:43 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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 |
To the developers/maintainers of the PICS package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1470/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PICS 2.43.0 (landing page) Renan Sauteraud
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
Package: PICS |
Version: 2.43.0 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PICS.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings PICS_2.43.0.tar.gz |
StartedAt: 2022-12-29 02:19:09 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 02:21:36 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 147.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PICS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PICS.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings PICS_2.43.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/PICS.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'PICS/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'PICS' version '2.43.0' * 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 whether package 'PICS' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 12.2.0' * 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 R 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 ... NOTE Package has both 'src/Makevars.in' and 'src/Makevars'. Installation with --no-configure' is unlikely to work. If you intended 'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win' otherwise remove it. If 'configure' created 'src/Makevars', you need a 'cleanup' script. * 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 for x64 is not available File 'F:/biocbuild/bbs-3.17-bioc/R/library/PICS/libs/x64/PICS.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) 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 in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/PICS.Rcheck/00check.log' for details.
PICS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL PICS ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'PICS' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs using C compiler: 'gcc.exe (GCC) 12.2.0' gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:421:25: warning: 'firstFit' may be used uninitialized [-Wmaybe-uninitialized] 421 | SEXP ans, temp, firstFit; | ^~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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 -s -static-libgcc -o PICS.dll tmp.def pics.o segment.o -lws2_32 -L/x64/lib -lgsl -lgslcblas -lm -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-PICS/00new/PICS/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 (PICS)
PICS.Rcheck/PICS-Ex.timings
name | user | system | elapsed | |
segmentPICS | 0.80 | 0.00 | 0.84 | |
setParaPrior | 0 | 0 | 0 | |