Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-16 11:41 -0400 (Fri, 16 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 983/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
iBMQ 1.45.0 (landing page) Greg Imholte
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | ... NOT SUPPORTED ... | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the iBMQ package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iBMQ.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: iBMQ |
Version: 1.45.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iBMQ.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings iBMQ_1.45.0.tar.gz |
StartedAt: 2024-08-16 01:43:20 -0400 (Fri, 16 Aug 2024) |
EndedAt: 2024-08-16 01:44:26 -0400 (Fri, 16 Aug 2024) |
EllapsedTime: 66.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: iBMQ.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iBMQ.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings iBMQ_1.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/iBMQ.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'iBMQ/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'iBMQ' version '1.45.0' * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'iBMQ' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 ... NOTE Packages in Depends field not imported from: 'Biobase' 'ggplot2' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE eqtlMcmc: no visible global function definition for 'is' eqtlMcmc: no visible global function definition for 'exprs' Undefined global functions or variables: exprs is Consider adding importFrom("methods", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/iBMQ/libs/x64/iBMQ.dll': Found '_assert', possibly from 'assert' (C) Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed eqtlClassifier 7.97 0.18 8.16 * 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: 5 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/iBMQ.Rcheck/00check.log' for details.
iBMQ.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL iBMQ ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'iBMQ' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ARS.c -o ARS.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RngStream.c -o RngStream.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c iBMQ_common.c -o iBMQ_common.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c main_parallel_sparse.c -o main_parallel_sparse.o main_parallel_sparse.c: In function 'iBMQ_main': main_parallel_sparse.c:255:33: warning: 'Pfile' may be used uninitialized [-Wmaybe-uninitialized] 255 | store_mcmc_output(Afile, Bfile, Pfile, Mufile, Sig2file, Cfile, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 256 | n_snps, n_genes, A, B, P, Mu, Sig2, C); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main_parallel_sparse.c:83:15: note: 'Pfile' was declared here 83 | FILE *Pfile, *Afile, *Bfile, *Mufile, *Sig2file, *Cfile; | ^~~~~ main_parallel_sparse.c:255:33: warning: 'Afile' may be used uninitialized [-Wmaybe-uninitialized] 255 | store_mcmc_output(Afile, Bfile, Pfile, Mufile, Sig2file, Cfile, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 256 | n_snps, n_genes, A, B, P, Mu, Sig2, C); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main_parallel_sparse.c:83:23: note: 'Afile' was declared here 83 | FILE *Pfile, *Afile, *Bfile, *Mufile, *Sig2file, *Cfile; | ^~~~~ main_parallel_sparse.c:255:33: warning: 'Bfile' may be used uninitialized [-Wmaybe-uninitialized] 255 | store_mcmc_output(Afile, Bfile, Pfile, Mufile, Sig2file, Cfile, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 256 | n_snps, n_genes, A, B, P, Mu, Sig2, C); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main_parallel_sparse.c:83:31: note: 'Bfile' was declared here 83 | FILE *Pfile, *Afile, *Bfile, *Mufile, *Sig2file, *Cfile; | ^~~~~ main_parallel_sparse.c:255:33: warning: 'Mufile' may be used uninitialized [-Wmaybe-uninitialized] 255 | store_mcmc_output(Afile, Bfile, Pfile, Mufile, Sig2file, Cfile, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 256 | n_snps, n_genes, A, B, P, Mu, Sig2, C); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main_parallel_sparse.c:83:39: note: 'Mufile' was declared here 83 | FILE *Pfile, *Afile, *Bfile, *Mufile, *Sig2file, *Cfile; | ^~~~~~ main_parallel_sparse.c:255:33: warning: 'Sig2file' may be used uninitialized [-Wmaybe-uninitialized] 255 | store_mcmc_output(Afile, Bfile, Pfile, Mufile, Sig2file, Cfile, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 256 | n_snps, n_genes, A, B, P, Mu, Sig2, C); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main_parallel_sparse.c:83:48: note: 'Sig2file' was declared here 83 | FILE *Pfile, *Afile, *Bfile, *Mufile, *Sig2file, *Cfile; | ^~~~~~~~ main_parallel_sparse.c:255:33: warning: 'Cfile' may be used uninitialized [-Wmaybe-uninitialized] 255 | store_mcmc_output(Afile, Bfile, Pfile, Mufile, Sig2file, Cfile, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 256 | n_snps, n_genes, A, B, P, Mu, Sig2, C); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main_parallel_sparse.c:83:59: note: 'Cfile' was declared here 83 | FILE *Pfile, *Afile, *Bfile, *Mufile, *Sig2file, *Cfile; | ^~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c main_parallel_sparse_constC.c -o main_parallel_sparse_constC.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c norm_gamma_generation.c -o norm_gamma_generation.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sparse.c -o sparse.o gcc -shared -s -static-libgcc -o iBMQ.dll tmp.def ARS.o RngStream.o iBMQ_common.o main_parallel_sparse.o main_parallel_sparse_constC.o norm_gamma_generation.o sparse.o -L/x64/lib -lgsl -lgslcblas -lm -fopenmp -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-iBMQ/00new/iBMQ/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (iBMQ)
iBMQ.Rcheck/iBMQ-Ex.timings
name | user | system | elapsed | |
PPA.liver | 0.16 | 0.02 | 0.17 | |
calculateThreshold | 0.32 | 0.02 | 0.34 | |
eqtlClassifier | 7.97 | 0.18 | 8.16 | |
eqtlFinder | 0.43 | 0.08 | 0.50 | |
eqtlMcmc | 0.04 | 0.03 | 0.08 | |
gene | 0.03 | 0.05 | 0.08 | |
genepos | 0.00 | 0.01 | 0.01 | |
genotype.liver | 0.00 | 0.02 | 0.02 | |
hotspotFinder | 0.50 | 0.09 | 0.60 | |
map.liver | 0 | 0 | 0 | |
phenotype.liver | 0.05 | 0.00 | 0.05 | |
probe.liver | 0.02 | 0.00 | 0.01 | |
snp | 0.01 | 0.01 | 0.04 | |
snppos | 0 | 0 | 0 | |