Multiple platform build/check report for BioC 3.11 - CHECK report for cmapR on machv2

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### Running command:
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###   /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

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


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

name	user	system	elapsed
GCT	0.334	0.033	0.391
align_matrices	0.004	0.002	0.006
annotate_gct	0.293	0.035	0.341
append_dim	0.000	0.001	0.001
check_colnames	0.002	0.003	0.005
check_dups	0.001	0.000	0.001
distil	0.003	0.000	0.003
extract_gct	0.189	0.009	0.206
fix_datatypes	0.039	0.002	0.042
ids	0.543	0.006	0.575
is.wholenumber	0.001	0.001	0.001
lxb2mat	0.014	0.003	0.019
mat	0.002	0.001	0.002
melt_gct	2.312	0.115	2.522
merge_gct	0.237	0.010	0.260
merge_with_precedence	0.011	0.001	0.014
meta	0.003	0.000	0.005
na_pad_matrix	0.003	0.006	0.009
parse_gctx	0.389	0.018	0.427
parse_gmt	0.056	0.004	0.063
parse_gmx	0.030	0.002	0.033
parse_grp	0.005	0.001	0.006
process_ids	0.010	0.002	0.011
rank_gct	0.139	0.015	0.160
read_gctx_ids	0.013	0.003	0.017
read_gctx_meta	0.233	0.026	0.270
robust_zscore	0.002	0.001	0.003
subset_gct	0.118	0.014	0.140
threshold	0.001	0.000	0.001
transpose_gct	0.090	0.003	0.099
update_gctx	0	0	0
write_gct	2.525	0.243	2.887
write_gctx	0.254	0.028	0.283
write_gctx_meta	0.000	0.000	0.001
write_gmt	0.001	0.000	0.001
write_grp	0.000	0.000	0.001
write_tbl	0.000	0.000	0.001

CHECK report for cmapR on machv2

Summary

Command output

Installation output

Tests output

Example timings