Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:37:36 -0400 (Wed, 15 Apr 2020).
Package 1133/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
NarrowPeaks 1.30.0 Pedro Madrigal
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK |
Package: NarrowPeaks |
Version: 1.30.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NarrowPeaks.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NarrowPeaks_1.30.0.tar.gz |
StartedAt: 2020-04-15 04:11:32 -0400 (Wed, 15 Apr 2020) |
EndedAt: 2020-04-15 04:14:08 -0400 (Wed, 15 Apr 2020) |
EllapsedTime: 156.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: NarrowPeaks.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NarrowPeaks.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NarrowPeaks_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/NarrowPeaks.Rcheck’ * using R version 3.6.3 (2020-02-29) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘NarrowPeaks/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘NarrowPeaks’ version ‘1.30.0’ * 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 ‘NarrowPeaks’ can be installed ... WARNING Found the following significant warnings: wig2CSARScore.c:240:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] wig2CSARScore.c:246:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] wig2CSARScore.c:267:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] wig2CSARScore.c:273:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] wig2CSARScore.c:352:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] wig2CSARScore.c:359:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] wig2CSARScore.c:380:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] wig2CSARScore.c:387:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] See ‘/Users/biocbuild/bbs-3.10-bioc/meat/NarrowPeaks.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘GenomicRanges’ ‘CSAR’ 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 Package in Depends field not imported from: ‘splines’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE narrowpeaksDiff: no visible global function definition for ‘read.table’ Undefined global functions or variables: read.table Consider adding importFrom("utils", "read.table") 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 Examples with CPU or elapsed time > 5s user system elapsed NarrowPeaks-package 13.661 2.702 16.488 narrowpeaks 12.461 2.882 15.648 * 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: 1 WARNING, 4 NOTEs See ‘/Users/biocbuild/bbs-3.10-bioc/meat/NarrowPeaks.Rcheck/00check.log’ for details.
NarrowPeaks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL NarrowPeaks ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘NarrowPeaks’ ... ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c wig2CSARScore.c -o wig2CSARScore.o wig2CSARScore.c:240:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] for(i=i;i<x+span_c;i++){ ~^~ wig2CSARScore.c:246:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] for(i=i;i<=chrL[m];i++) ~^~ wig2CSARScore.c:267:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] for(i=i;i<x+span_c;i++){ ~^~ wig2CSARScore.c:273:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] for(i=i;i<=chrL[m];i++) ~^~ wig2CSARScore.c:352:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] for(i=i;i<start_c+span_c;i++){ ~^~ wig2CSARScore.c:359:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] for(i=i;i<=chrL[m];i++) ~^~ wig2CSARScore.c:380:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] for(i=i;i<start_c+span_c;i++){ ~^~ wig2CSARScore.c:387:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] for(i=i;i<=chrL[m];i++) ~^~ 8 warnings generated. clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c wig2CSARScore_R_wrapper.c -o wig2CSARScore_R_wrapper.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 NarrowPeaks.so wig2CSARScore.o wig2CSARScore_R_wrapper.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-NarrowPeaks/00new/NarrowPeaks/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 (NarrowPeaks)
NarrowPeaks.Rcheck/NarrowPeaks-Ex.timings
name | user | system | elapsed | |
NarrowPeaks-package | 13.661 | 2.702 | 16.488 | |
narrowpeaks | 12.461 | 2.882 | 15.648 | |
narrowpeaksDiff | 0.001 | 0.001 | 0.000 | |
wig2CSARScore | 2.912 | 0.600 | 3.567 | |
wigfile_test | 0.002 | 0.001 | 0.002 | |