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CHECK report for PAST on malbec2

This page was generated on 2019-10-16 12:18:27 -0400 (Wed, 16 Oct 2019).

Package 1171/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PAST 1.0.1
Thrash Adam
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/PAST
Branch: RELEASE_3_9
Last Commit: bb44d41
Last Changed Date: 2019-08-07 10:23:22 -0400 (Wed, 07 Aug 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

Summary

Package: PAST
Version: 1.0.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PAST.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PAST_1.0.1.tar.gz
StartedAt: 2019-10-16 03:47:03 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:01:51 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 888.4 seconds
RetCode: 0
Status:  OK 
CheckDir: PAST.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PAST.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PAST_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/PAST.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PAST’ version ‘1.0.1’
* 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 ‘PAST’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
assign_SNPs_to_genes: no visible binding for global variable
  ‘Marker_original.x’
find_pathway_significance: no visible binding for global variable
  ‘gene_id’
load_GWAS_data: no visible binding for global variable ‘Chr’
load_GWAS_data: no visible binding for global variable ‘Pos’
Undefined global functions or variables:
  Chr Marker_original.x Pos gene_id
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
plot_pathways             22.606  1.309 243.443
find_pathway_significance 21.052  0.987 242.619
assign_SNPs_to_genes      18.213  0.711 199.522
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/PAST.Rcheck/00check.log’
for details.



Installation output

PAST.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL PAST
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘PAST’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PAST)

Tests output


Example timings

PAST.Rcheck/PAST-Ex.timings

nameusersystemelapsed
assign_SNPs_to_genes 18.213 0.711199.522
find_pathway_significance 21.052 0.987242.619
load_GWAS_data0.1780.0000.178
load_LD0.8880.0250.920
plot_pathways 22.606 1.309243.443