Pedro Madrigal
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/NarrowPeaks |
| Branch: RELEASE_3_10 |
| Last Commit: 8feaaa8 |
| Last Changed Date: 2019-10-29 13:08:28 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
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 |
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### Running command:
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### /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
###
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* 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
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL NarrowPeaks
###
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* 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 | |