Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:41 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 14/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ADaCGH2 2.47.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
To the developers/maintainers of the ADaCGH2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ADaCGH2.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: ADaCGH2 |
Version: 2.47.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ADaCGH2.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings ADaCGH2_2.47.0.tar.gz |
StartedAt: 2024-12-23 22:01:32 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 22:05:59 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 266.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ADaCGH2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ADaCGH2.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings ADaCGH2_2.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/ADaCGH2.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 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 'ADaCGH2/DESCRIPTION' ... OK * this is package 'ADaCGH2' version '2.47.0' * 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 'ADaCGH2' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.3.0' * 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 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'E:/biocbuild/bbs-3.21-bioc/R/library/ADaCGH2/libs/x64/ADaCGH2.dll': Found '_exit', possibly from '_exit' (C) 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 sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed pChromPlot 30.11 0.09 30.25 pSegment 25.58 0.00 25.57 outputToCGHregions 14.42 0.11 15.13 inputToADaCGH 7.15 0.06 7.32 * 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: 1 NOTE See 'E:/biocbuild/bbs-3.21-bioc/meat/ADaCGH2.Rcheck/00check.log' for details.
ADaCGH2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL ADaCGH2 ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'ADaCGH2' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c r_haarseg.c -o r_haarseg.o r_haarseg.c: In function 'ad_HaarConv': r_haarseg.c:65:12: warning: unused variable 'totalNorm' [-Wunused-variable] 65 | double totalNorm; | ^~~~~~~~~ r_haarseg.c: In function 'ad_FindLocalPeaks': r_haarseg.c:152:43: warning: "/*" within comment [-Wcomment] 152 | }/* for j */ | r_haarseg.c:176:43: warning: "/*" within comment [-Wcomment] 176 | }/* for j */ | r_haarseg.c:128:16: warning: unused variable 'j' [-Wunused-variable] 128 | int k,j; | ^ r_haarseg.c: In function 'ad_HaarConv': r_haarseg.c:98:26: warning: 'lowWeightSum' may be used uninitialized [-Wmaybe-uninitialized] 98 | lowWeightSum += weight[k-1] - weight[lowEnd]; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ r_haarseg.c:59:12: note: 'lowWeightSum' was declared here 59 | double lowWeightSum; | ^~~~~~~~~~~~ r_haarseg.c:96:26: warning: 'lowNonNormed' may be used uninitialized [-Wmaybe-uninitialized] 96 | lowNonNormed += signal[lowEnd]*weight[lowEnd] - signal[k-1]*weight[k-1]; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ r_haarseg.c:63:12: note: 'lowNonNormed' was declared here 63 | double lowNonNormed; | ^~~~~~~~~~~~ r_haarseg.c:97:27: warning: 'highNonNormed' may be used uninitialized [-Wmaybe-uninitialized] 97 | highNonNormed += signal[highEnd]*weight[highEnd] - signal[k-1]*weight[k-1]; | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ r_haarseg.c:64:12: note: 'highNonNormed' was declared here 64 | double highNonNormed; | ^~~~~~~~~~~~~ gcc -shared -s -static-libgcc -o ADaCGH2.dll tmp.def init.o r_haarseg.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/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-ADaCGH2/00new/ADaCGH2/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 (ADaCGH2)
ADaCGH2.Rcheck/ADaCGH2-Ex.timings
name | user | system | elapsed | |
cutFile | 0 | 0 | 0 | |
inputToADaCGH | 7.15 | 0.06 | 7.32 | |
outputToCGHregions | 14.42 | 0.11 | 15.13 | |
pChromPlot | 30.11 | 0.09 | 30.25 | |
pSegment | 25.58 | 0.00 | 25.57 | |