Philippe Hupe
| Snapshot Date: 2025-03-16 13:40 -0400 (Sun, 16 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/GLAD |
| git_branch: devel |
| git_last_commit: 1c16508 |
| git_last_commit_date: 2024-10-29 09:23:29 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
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 |
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###
### 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
###
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* 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
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### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL GLAD
###
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* 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 | |