Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:31:24 -0400 (Thu, 12 Apr 2018).
Package 11/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
aCGH 1.56.0 Peter Dimitrov
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | ![]() |
Package: aCGH |
Version: 1.56.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings aCGH_1.56.0.tar.gz |
StartedAt: 2018-04-12 00:08:40 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 00:09:56 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 75.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: aCGH.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings aCGH_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/aCGH.Rcheck’ * using R version 3.4.4 (2018-03-15) * 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 ‘1.56.0’ * 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 ... OK * 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 ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.6-bioc/meat/aCGH.Rcheck/00check.log’ for details.
aCGH.Rcheck/00install.out
* installing *source* package ‘aCGH’ ... ** libs clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -g3 -I/usr/local/include -fPIC -Wall -g -O2 -c hmm.cpp -o hmm.o clang++ -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 /Users/biocbuild/bbs-3.6-bioc/meat/aCGH.Rcheck/aCGH/libs ** R ** data ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (aCGH)
aCGH.Rcheck/aCGH-Ex.timings
name | user | system | elapsed | |
aCGH | 2.148 | 0.113 | 2.299 | |
aCGH.process | 0.079 | 0.001 | 0.084 | |
aCGH.read.Sprocs | 0.312 | 0.004 | 0.324 | |
clusterGenome | 1.180 | 0.067 | 1.276 | |
colorectal | 0.482 | 0.024 | 0.517 | |
fga.func | 0.410 | 0.017 | 0.432 | |
find.hmm.states | 0.399 | 0.014 | 0.414 | |
gainLoss | 0.917 | 0.025 | 0.944 | |
heatmap | 0.338 | 0.022 | 0.362 | |
impute.HMM | 0.397 | 0.007 | 0.406 | |
impute.lowess | 0.107 | 0.002 | 0.108 | |
mergeLevels | 0.080 | 0.002 | 0.082 | |
plotFreqStat | 3.425 | 0.037 | 3.482 | |
plotGenome | 1.139 | 0.058 | 1.237 | |
plotHmmStates | 0.225 | 0.027 | 0.253 | |
plotSummaryProfile | 0.826 | 0.046 | 0.890 | |
summarize.clones | 0.252 | 0.027 | 0.279 | |
threshold.func | 0.158 | 0.019 | 0.177 | |