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CHECK report for cmapR on machv2

This page was generated on 2020-10-17 11:58:15 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE cmapR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 325/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cmapR 1.0.0
Ted Natoli
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/cmapR
Branch: RELEASE_3_11
Last Commit: c5f43d3
Last Changed Date: 2020-04-27 15:34:53 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cmapR
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cmapR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cmapR_1.0.0.tar.gz
StartedAt: 2020-10-16 23:50:02 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:54:23 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 261.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: cmapR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cmapR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cmapR_1.0.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/cmapR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cmapR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cmapR’ version ‘1.0.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .dockerignore
  docs/build/html/.buildinfo
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 ‘cmapR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   2.1Mb
* 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 ... NOTE
subset_gct,GCT: warning in meta(g, dim = "col"): partial argument match
  of 'dim' to 'dimension'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘ids<-’ ‘mat<-’ ‘meta<-’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/cmapR.Rcheck/00check.log’
for details.



Installation output

cmapR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cmapR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘cmapR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (cmapR)

Tests output

cmapR.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(cmapR)
> 
> test_check("cmapR")
Saving file to  foo.gct 
Dimensions of matrix: [10x5]
Setting precision to 4
Saved.
Saving file to  foo.gct 
Dimensions of matrix: [10x5]
Setting precision to 4
Saved.
Saving file to  ./foo_n272x978.gct 
Dimensions of matrix: [978x272]
Setting precision to 4
Saved.
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 165 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 23.105   1.221  24.972 

Example timings

cmapR.Rcheck/cmapR-Ex.timings

nameusersystemelapsed
GCT0.3340.0330.391
align_matrices0.0040.0020.006
annotate_gct0.2930.0350.341
append_dim0.0000.0010.001
check_colnames0.0020.0030.005
check_dups0.0010.0000.001
distil0.0030.0000.003
extract_gct0.1890.0090.206
fix_datatypes0.0390.0020.042
ids0.5430.0060.575
is.wholenumber0.0010.0010.001
lxb2mat0.0140.0030.019
mat0.0020.0010.002
melt_gct2.3120.1152.522
merge_gct0.2370.0100.260
merge_with_precedence0.0110.0010.014
meta0.0030.0000.005
na_pad_matrix0.0030.0060.009
parse_gctx0.3890.0180.427
parse_gmt0.0560.0040.063
parse_gmx0.0300.0020.033
parse_grp0.0050.0010.006
process_ids0.0100.0020.011
rank_gct0.1390.0150.160
read_gctx_ids0.0130.0030.017
read_gctx_meta0.2330.0260.270
robust_zscore0.0020.0010.003
subset_gct0.1180.0140.140
threshold0.0010.0000.001
transpose_gct0.0900.0030.099
update_gctx000
write_gct2.5250.2432.887
write_gctx0.2540.0280.283
write_gctx_meta0.0000.0000.001
write_gmt0.0010.0000.001
write_grp0.0000.0000.001
write_tbl0.0000.0000.001