Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:35 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the ADaCGH2 package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 14/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ADaCGH2 2.39.0 (landing page) Ramon Diaz-Uriarte
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: ADaCGH2 |
Version: 2.39.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ADaCGH2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ADaCGH2_2.39.0.tar.gz |
StartedAt: 2023-02-27 19:56:06 -0000 (Mon, 27 Feb 2023) |
EndedAt: 2023-02-27 20:04:32 -0000 (Mon, 27 Feb 2023) |
EllapsedTime: 506.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ADaCGH2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ADaCGH2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ADaCGH2_2.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ADaCGH2.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘ADaCGH2/DESCRIPTION’ ... OK * this is package ‘ADaCGH2’ version ‘2.39.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘ADaCGH2’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ * 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 R 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 is not available * 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 pSegment 44.313 6.592 43.641 pChromPlot 30.536 18.713 24.702 outputToCGHregions 30.337 3.089 19.419 inputToADaCGH 7.264 1.118 8.186 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘ADaCGH2.Rnw’ using ‘latin1’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/ADaCGH2.Rcheck/00check.log’ for details.
ADaCGH2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ADaCGH2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘ADaCGH2’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -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:97:27: warning: ‘highNonNormed’ may be used uninitialized in this function [-Wmaybe-uninitialized] 97 | highNonNormed += signal[highEnd]*weight[highEnd] - signal[k-1]*weight[k-1]; | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ r_haarseg.c:98:26: warning: ‘lowWeightSum’ may be used uninitialized in this function [-Wmaybe-uninitialized] 98 | lowWeightSum += weight[k-1] - weight[lowEnd]; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ r_haarseg.c:99:27: warning: ‘highWeightSum’ may be used uninitialized in this function [-Wmaybe-uninitialized] 99 | highWeightSum += weight[highEnd] - weight[k-1]; | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ r_haarseg.c:96:26: warning: ‘lowNonNormed’ may be used uninitialized in this function [-Wmaybe-uninitialized] 96 | lowNonNormed += signal[lowEnd]*weight[lowEnd] - signal[k-1]*weight[k-1]; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o ADaCGH2.so init.o r_haarseg.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-ADaCGH2/00new/ADaCGH2/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** 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 | 0.046 | 0.028 | 2.069 | |
inputToADaCGH | 7.264 | 1.118 | 8.186 | |
outputToCGHregions | 30.337 | 3.089 | 19.419 | |
pChromPlot | 30.536 | 18.713 | 24.702 | |
pSegment | 44.313 | 6.592 | 43.641 | |