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This page was generated on 2025-03-17 11:37 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R 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 875/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GLAD 2.71.0  (landing page)
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)
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for GLAD on palomino7

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.

raw results


Summary

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

Command output

##############################################################################
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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
###
##############################################################################
##############################################################################


* 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.


Installation output

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)

Tests output


Example timings

GLAD.Rcheck/GLAD-Ex.timings

nameusersystemelapsed
ChrNumeric000
ColorBar0.030.000.03
arrayCGH0.050.000.05
arrayPersp000
arrayPlot0.160.010.17
as.data.frame.profileCGH0.210.020.24
as.profileCGH0.070.000.06
bladder0.000.030.03
cytoband0.000.030.03
daglad0.780.020.80
glad0.540.040.59
hclust0.040.000.03
myPalette0.010.000.02
plotProfile0.880.020.89
profileCGH0.070.000.08
snijders0.050.000.04
veltman0.080.090.18