Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 12:48:57 -0400 (Tue, 09 Apr 2019).
Package 13/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
aCGH 1.61.0 Peter Dimitrov
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ![]() | ||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | ![]() | ||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: aCGH |
Version: 1.61.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:aCGH.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings aCGH_1.61.0.tar.gz |
StartedAt: 2019-04-08 23:43:22 -0400 (Mon, 08 Apr 2019) |
EndedAt: 2019-04-08 23:45:23 -0400 (Mon, 08 Apr 2019) |
EllapsedTime: 121.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: aCGH.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:aCGH.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings aCGH_1.61.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/aCGH.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘aCGH/DESCRIPTION’ ... OK * this is package ‘aCGH’ version ‘1.61.0’ * 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 ... NOTE Malformed Title field: should not end in a period. Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘cluster’ ‘multtest’ ‘survival’ A package should be listed in only one of these fields. * 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 ... NOTE Missing or unexported object: ‘multtest::.mt.naNUM’ * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: [.aCGH dim.aCGH plot.aCGH print.aCGH row.names.aCGH row.names<-.aCGH subset.hmm subset.hmm.merged summary.aCGH 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 ... NOTE aCGH.read.Sprocs: warning in read.table(fnames[1], h = TRUE, sep = "\t", quote = "", comment.char = "", fill = TRUE, blank.lines.skip = FALSE): partial argument match of 'h' to 'header' aCGH.read.Sprocs: warning in read.table(latest.mapping.file, sep = "\t", h = TRUE, quote = "", comment.char = ""): partial argument match of 'h' to 'header' plotCGH.func: warning in close.screen(all = TRUE): partial argument match of 'all' to 'all.screens' plotCGH.hmm.func: warning in close.screen(all = TRUE): partial argument match of 'all' to 'all.screens' plotFreqStat: warning in axis(side = 1, at = kb.loc[ind][1], label = "", tick = FALSE): partial argument match of 'label' to 'labels' plotGenome: warning in axis(side = 1, at = clone.genomepos[1]/1000, label = "", tick = FALSE): partial argument match of 'label' to 'labels' read.Sproc.files : <anonymous>: warning in read.table(fname, h = TRUE, sep = "\t", quote = "", comment.char = "", fill = TRUE, blank.lines.skip = FALSE, dec = "."): partial argument match of 'h' to 'header' states.hmm.func: warning in matrix(res$filtered.cond.probs, nr = k): partial argument match of 'nr' to 'nrow' states.hmm.func: warning in matrix(res$gamma, nr = k): partial argument match of 'nr' to 'nrow' plotSummaryProfile: no visible binding for global variable ‘numchromgain’ plotSummaryProfile: no visible binding for global variable ‘numchromloss’ plotSummaryProfile: no visible binding for global variable ‘numtrans’ plotSummaryProfile: no visible binding for global variable ‘numtrans.binary’ plotSummaryProfile: no visible binding for global variable ‘numaber’ plotSummaryProfile: no visible binding for global variable ‘numamplif’ plotSummaryProfile: no visible binding for global variable ‘numamplif.binary’ plotSummaryProfile: no visible binding for global variable ‘numamplicon’ plotSummaryProfile: no visible binding for global variable ‘sizeamplicon’ Undefined global functions or variables: numaber numamplicon numamplif numamplif.binary numchromgain numchromloss numtrans numtrans.binary sizeamplicon * 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 compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed plotFreqStat 5.508 0.181 5.729 * 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/aCGH.Rcheck/00check.log’ for details.
aCGH.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL aCGH ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘aCGH’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -g3 -I/usr/local/include -fPIC -Wall -g -O2 -c hmm.cpp -o hmm.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o aCGH.so hmm.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/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 | 2.607 | 0.296 | 2.920 | |
aCGH.process | 0.063 | 0.004 | 0.067 | |
aCGH.read.Sprocs | 0.366 | 0.036 | 0.407 | |
clusterGenome | 1.314 | 0.184 | 1.515 | |
colorectal | 0.594 | 0.055 | 0.651 | |
fga.func | 0.345 | 0.048 | 0.393 | |
find.hmm.states | 0.752 | 0.074 | 0.826 | |
gainLoss | 0.856 | 0.101 | 0.960 | |
heatmap | 0.737 | 0.083 | 0.828 | |
impute.HMM | 0.672 | 0.044 | 0.756 | |
impute.lowess | 0.136 | 0.019 | 0.178 | |
mergeLevels | 0.192 | 0.040 | 0.233 | |
plotFreqStat | 5.508 | 0.181 | 5.729 | |
plotGenome | 1.600 | 0.173 | 1.857 | |
plotHmmStates | 0.300 | 0.058 | 0.365 | |
plotSummaryProfile | 1.438 | 0.107 | 1.603 | |
summarize.clones | 0.294 | 0.050 | 0.350 | |
threshold.func | 0.238 | 0.063 | 0.303 | |