Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:34 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the aCGH package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/aCGH.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 13/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
aCGH 1.70.0 (landing page) Peter Dimitrov
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: aCGH |
Version: 1.70.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:aCGH.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings aCGH_1.70.0.tar.gz |
StartedAt: 2021-10-14 08:49:31 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 08:50:35 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 63.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: aCGH.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:aCGH.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings aCGH_1.70.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/aCGH.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘aCGH/DESCRIPTION’ ... OK * this is package ‘aCGH’ version ‘1.70.0’ * 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 ‘aCGH’ can be installed ... OK * 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 ... NOTE Found the following apparent S3 methods exported but not registered: row.names.aCGH row.names<-.aCGH subset.hmm subset.hmm.merged See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * 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 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/aCGH.Rcheck/00check.log’ for details.
aCGH.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL aCGH ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘aCGH’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DUSEDOUBLE -g3 -I/usr/local/include -fpic -g -O2 -Wall -c hmm.cpp -o hmm.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o aCGH.so hmm.o -lm -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-aCGH/00new/aCGH/libs ** 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 ** 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 (aCGH)
aCGH.Rcheck/aCGH-Ex.timings
name | user | system | elapsed | |
aCGH | 1.193 | 0.084 | 1.278 | |
aCGH.process | 0.032 | 0.000 | 0.032 | |
aCGH.read.Sprocs | 0.137 | 0.000 | 0.143 | |
clusterGenome | 1.033 | 0.048 | 1.081 | |
colorectal | 0.444 | 0.012 | 0.456 | |
fga.func | 0.194 | 0.008 | 0.203 | |
find.hmm.states | 0.416 | 0.016 | 0.432 | |
gainLoss | 0.566 | 0.016 | 0.583 | |
heatmap | 0.440 | 0.020 | 0.459 | |
impute.HMM | 0.284 | 0.000 | 0.285 | |
impute.lowess | 0.047 | 0.012 | 0.059 | |
mergeLevels | 0.085 | 0.004 | 0.090 | |
plotFreqStat | 3.110 | 0.032 | 3.143 | |
plotGenome | 1.246 | 0.028 | 1.274 | |
plotHmmStates | 0.228 | 0.036 | 0.264 | |
plotSummaryProfile | 0.747 | 0.016 | 0.764 | |
summarize.clones | 0.203 | 0.012 | 0.215 | |
threshold.func | 0.171 | 0.012 | 0.182 | |