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CHECK report for PrInCE on merida2

This page was generated on 2019-04-09 13:39:22 -0400 (Tue, 09 Apr 2019).

Package 1223/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PrInCE 0.99.13
Michael Skinnider
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/PrInCE
Branch: master
Last Commit: 017fd69
Last Changed Date: 2019-03-12 19:10:59 -0400 (Tue, 12 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: PrInCE
Version: 0.99.13
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PrInCE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PrInCE_0.99.13.tar.gz
StartedAt: 2019-04-09 02:59:44 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:03:20 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 216.0 seconds
RetCode: 0
Status:  OK 
CheckDir: PrInCE.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PrInCE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PrInCE_0.99.13.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/PrInCE.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PrInCE/DESCRIPTION’ ... OK
* this is package ‘PrInCE’ version ‘0.99.13’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PrInCE’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
calculate_precision  6.831  0.384   7.239
predict_ensemble     6.492  0.379   6.897
PrInCE               6.471  0.380   6.866
predict_interactions 6.333  0.354   6.702
threshold_precision  5.127  0.315   5.461
* 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: OK


Installation output

PrInCE.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PrInCE
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘PrInCE’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: PrInCE
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PrInCE)

Tests output


Example timings

PrInCE.Rcheck/PrInCE-Ex.timings

nameusersystemelapsed
PrInCE6.4710.3806.866
adjacency_matrix_from_data_frame0.0020.0000.002
adjacency_matrix_from_list1.2750.0281.308
build_gaussians0.7710.0400.813
calculate_precision6.8310.3847.239
check_gaussians0.1530.0030.156
choose_gaussians0.2590.0030.263
clean_profile0.0680.0010.070
clean_profiles0.0570.0020.059
co_apex0.1630.0020.166
detect_complexes0.1690.0030.173
filter_profiles0.4350.0270.464
fit_curve0.2310.0040.236
fit_gaussians0.2480.0040.251
impute_neighbors0.0600.0010.062
is_unweighted1.4660.0261.501
is_weighted1.4590.0091.474
make_initial_conditions0.0580.0010.059
make_labels1.3440.0061.352
match_matrix_dimensions1.9560.0051.967
predict_ensemble6.4920.3796.897
predict_interactions6.3330.3546.702
threshold_precision5.1270.3155.461