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This page was generated on 2021-10-15 15:06:41 -0400 (Fri, 15 Oct 2021).

CHECK results for MACPET on machv2

To the developers/maintainers of the MACPET package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MACPET.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1016/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MACPET 1.12.0  (landing page)
Ioannis Vardaxis
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/MACPET
git_branch: RELEASE_3_13
git_last_commit: 2e34842
git_last_commit_date: 2021-05-19 12:33:30 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MACPET
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MACPET.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MACPET_1.12.0.tar.gz
StartedAt: 2021-10-14 20:35:32 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 20:41:06 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 334.7 seconds
RetCode: 0
Status:   OK  
CheckDir: MACPET.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MACPET.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MACPET_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/MACPET.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MACPET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MACPET’ version ‘1.12.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MACPET’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 R/sysdata.rda ... 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 (user + system) or elapsed time > 5s
            user system elapsed
MACPETUlt 10.603  0.843  15.869
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/MACPET.Rcheck/00check.log’
for details.



Installation output

MACPET.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MACPET
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘MACPET’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/bigmemory/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/bigmemory/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Stage_0_FastqFilteringSubFunctions.cpp -o Stage_0_FastqFilteringSubFunctions.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/bigmemory/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Stage_3_PeakFinderSubFunctions.cpp -o Stage_3_PeakFinderSubFunctions.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/bigmemory/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Stage_4_InteractionsSubFunctions.cpp -o Stage_4_InteractionsSubFunctions.o
clang++ -mmacosx-version-min=10.13 -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 MACPET.so RcppExports.o Stage_0_FastqFilteringSubFunctions.o Stage_3_PeakFinderSubFunctions.o Stage_4_InteractionsSubFunctions.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-MACPET/00new/MACPET/libs
** R
** 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 (MACPET)

Tests output


Example timings

MACPET.Rcheck/MACPET-Ex.timings

nameusersystemelapsed
AnalysisStatistics0.0910.0090.101
ConvertToPE_BAM4.4470.1904.653
ConvertToPSelf0.4770.0060.483
GetShortestPath0.1030.0010.106
GetSignInteractions0.1860.0030.188
MACPETUlt10.603 0.84315.869
PeaksToGRanges3.2721.4180.243
PeaksToNarrowPeak0.3770.0310.409
TagsToGInteractions0.1030.0120.115
exportPeaks0.0060.0020.007
plot3.9170.0553.979
summary0.6990.0130.713