Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-17 11:37 -0400 (Mon, 17 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
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 875/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GLAD 2.71.0 (landing page) Philippe Hupe
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | |||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the GLAD package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GLAD.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: GLAD |
Version: 2.71.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GLAD.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GLAD_2.71.0.tar.gz |
StartedAt: 2025-03-17 01:40:44 -0400 (Mon, 17 Mar 2025) |
EndedAt: 2025-03-17 01:41:46 -0400 (Mon, 17 Mar 2025) |
EllapsedTime: 62.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GLAD.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GLAD.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GLAD_2.71.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/GLAD.Rcheck' * using R Under development (unstable) (2025-03-01 r87860 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'GLAD/DESCRIPTION' ... OK * this is package 'GLAD' version '2.71.0' * 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 ... OK * checking for portable file names ... OK * checking whether package 'GLAD' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 14.2.0' * used C++ compiler: 'G__~1.EXE (GCC) 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... WARNING Missing or unexported object: 'aws::laws' * 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 ... WARNING checkRd: (5) as.profileCGH.Rd:25: \item in \value must have non-empty label checkRd: (-1) daglad.Rd:47: Escaped LaTeX specials: \$ checkRd: (5) daglad.Rd:182-183: \item in \value must have non-empty label checkRd: (-1) daglad.Rd:192-193: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) daglad.Rd:196-199: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) daglad.Rd:202-205: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) daglad.Rd:207-210: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) daglad.Rd:213-216: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) daglad.Rd:218: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) daglad.Rd:221-224: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) daglad.Rd:226-228: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) daglad.Rd:240: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) daglad.Rd:241: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) daglad.Rd:242-243: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) daglad.Rd:244: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) daglad.Rd:245: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) daglad.Rd:246: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) daglad.Rd:247-248: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) daglad.Rd:249: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (5) glad.Rd:152: \item in \value must have non-empty label checkRd: (-1) glad.Rd:159-160: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) glad.Rd:162-165: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) glad.Rd:168-171: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) glad.Rd:173-176: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) glad.Rd:178-179: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) glad.Rd:182-185: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) glad.Rd:187: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) glad.Rd:189-190: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) glad.Rd:192-193: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) glad.Rd:195-196: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) glad.Rd:204: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) glad.Rd:205: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) glad.Rd:206: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) glad.Rd:213: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) glad.Rd:214: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) glad.Rd:224: Lost braces in \itemize; meant \describe ? checkRd: (-1) glad.Rd:225: Lost braces in \itemize; meant \describe ? checkRd: (-1) glad.Rd:226: Lost braces in \itemize; meant \describe ? * 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 * checking sizes of PDF files under 'inst/doc' ... OK * 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: 2 WARNINGs, 1 NOTE See 'E:/biocbuild/bbs-3.21-bioc/meat/GLAD.Rcheck/00check.log' for details.
GLAD.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL GLAD ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'GLAD' ... ** this is package 'GLAD' version '2.71.0' ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs using C compiler: 'gcc.exe (GCC) 14.2.0' using C++ compiler: 'G__~1.EXE (GCC) 14.2.0' g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BkpInfo.cpp -o BkpInfo.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c HaarSeg.cpp -o HaarSeg.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MoveBkp.cpp -o MoveBkp.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c OutliersGNL.cpp -o OutliersGNL.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chrBreakpoints.cpp -o chrBreakpoints.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cutree.cpp -o cutree.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c daglad.cpp -o daglad.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c distance.cpp -o distance.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c filterBkp.cpp -o filterBkp.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c findCluster.cpp -o findCluster.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c glad-utils.cpp -o glad-utils.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hclust.cpp -o hclust.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c laws.c -o laws.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c loopRemove.cpp -o loopRemove.o g++ -std=gnu++17 -shared -s -static-libgcc -o GLAD.dll tmp.def BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -L/x64/lib -lgsl -lgslcblas -lm -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-GLAD/00new/GLAD/libs/x64 ** R ** data ** demo ** 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 (GLAD)
GLAD.Rcheck/GLAD-Ex.timings
name | user | system | elapsed | |
ChrNumeric | 0 | 0 | 0 | |
ColorBar | 0.03 | 0.00 | 0.03 | |
arrayCGH | 0.05 | 0.00 | 0.05 | |
arrayPersp | 0 | 0 | 0 | |
arrayPlot | 0.16 | 0.01 | 0.17 | |
as.data.frame.profileCGH | 0.21 | 0.02 | 0.24 | |
as.profileCGH | 0.07 | 0.00 | 0.06 | |
bladder | 0.00 | 0.03 | 0.03 | |
cytoband | 0.00 | 0.03 | 0.03 | |
daglad | 0.78 | 0.02 | 0.80 | |
glad | 0.54 | 0.04 | 0.59 | |
hclust | 0.04 | 0.00 | 0.03 | |
myPalette | 0.01 | 0.00 | 0.02 | |
plotProfile | 0.88 | 0.02 | 0.89 | |
profileCGH | 0.07 | 0.00 | 0.08 | |
snijders | 0.05 | 0.00 | 0.04 | |
veltman | 0.08 | 0.09 | 0.18 | |