Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-16 11:55:03 -0400 (Tue, 16 Apr 2019).
Package 293/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
CNTools 1.38.0 J. Zhang
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: CNTools |
Version: 1.38.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNTools_1.38.0.tar.gz |
StartedAt: 2019-04-15 23:07:20 -0400 (Mon, 15 Apr 2019) |
EndedAt: 2019-04-15 23:09:24 -0400 (Mon, 15 Apr 2019) |
EllapsedTime: 123.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CNTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNTools_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/CNTools.Rcheck’ * using R version 3.5.3 (2019-03-11) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CNTools/DESCRIPTION’ ... OK * this is package ‘CNTools’ version ‘1.38.0’ * 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 ‘CNTools’ 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. Malformed Description field: should contain one or more complete sentences. * 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 'library' or 'require' calls to packages already attached by Depends: ‘methods’ ‘tools’ Please remove these calls from your code. Packages in Depends field not imported from: ‘methods’ ‘tools’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' call which should be '::': ‘genefilter:::genefilter’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘getCommonSegValues’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘CNTools/R/zzz.R’: .onLoad calls: require("methods", quietly = TRUE) require("tools", quietly = TRUE) Package startup functions should not change the search path. See section ‘Good practice’ in '?.onAttach'. filterByMad: no visible binding for global variable ‘mad’ filterByMad: no visible global function definition for ‘quantile’ getPairCor : pair2Cor: no visible global function definition for ‘cor’ getPairDist : pair2Dist: no visible global function definition for ‘dist’ getPairDist: no visible global function definition for ‘as.dist’ getCor,RS: no visible global function definition for ‘cor’ getDist,RS: no visible global function definition for ‘dist’ Undefined global functions or variables: as.dist cor dist mad quantile Consider adding importFrom("stats", "as.dist", "cor", "dist", "mad", "quantile") to your NAMESPACE file. * 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 sizes of PDF files under ‘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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.8-bioc/meat/CNTools.Rcheck/00check.log’ for details.
CNTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CNTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘CNTools’ ... ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c getratios.c -o getratios.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 CNTools.so getratios.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/CNTools/libs ** R ** data ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘start’ in package ‘CNTools’ Creating a new generic function for ‘end’ in package ‘CNTools’ Creating a generic function for ‘genefilter’ from package ‘genefilter’ in package ‘CNTools’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (CNTools)
CNTools.Rcheck/CNTools-Ex.timings
name | user | system | elapsed | |
CNSeg-class | 1.425 | 0.025 | 1.489 | |
RS-class | 0.624 | 0.022 | 0.654 | |