Back to Multiple platform build/check report for BioC 3.14
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-19 13:07:49 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for cmapR on machv2


To the developers/maintainers of the cmapR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cmapR.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 346/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cmapR 1.6.0  (landing page)
Ted Natoli
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/cmapR
git_branch: RELEASE_3_14
git_last_commit: a9d9f50
git_last_commit_date: 2021-10-26 12:58:05 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: cmapR
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cmapR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cmapR_1.6.0.tar.gz
StartedAt: 2022-01-18 11:26:46 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 11:31:08 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 262.4 seconds
RetCode: 0
Status:   OK  
CheckDir: cmapR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cmapR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cmapR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/cmapR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.6.0’
* 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 ... 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 LazyData ... 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/cmapR.Rcheck/00check.log’
for details.



Installation output

cmapR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.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.
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (2)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 168 ]
> 
> proc.time()
   user  system elapsed 
 23.036   1.251  24.293 

Example timings

cmapR.Rcheck/cmapR-Ex.timings

nameusersystemelapsed
GCT0.3710.0260.402
align_matrices0.0040.0030.007
annotate_gct0.2770.0100.289
append_dim0.0010.0010.001
check_colnames0.0020.0020.004
check_dups0.0010.0000.001
distil0.0020.0000.002
extract_gct0.1080.0080.116
fix_datatypes0.0290.0020.032
ids0.0320.0030.036
is.wholenumber0.0010.0000.000
lxb2mat0.7780.0320.854
mat0.0020.0010.002
melt_gct2.4200.1252.554
merge_gct0.1870.0100.199
merge_with_precedence0.0110.0010.012
meta0.0020.0000.002
na_pad_matrix0.0020.0050.007
parse_gctx0.3740.0180.392
parse_gmt0.0460.0060.053
parse_gmx0.0260.0040.030
parse_grp0.0040.0010.006
process_ids0.0110.0020.013
rank_gct0.1220.0130.135
read_gctx_ids0.0140.0030.017
read_gctx_meta0.2330.0180.251
robust_zscore0.0010.0010.002
subset_gct0.0810.0130.092
threshold0.0000.0010.001
transpose_gct0.0820.0100.091
update_gctx0.0000.0010.000
write_gct2.0870.2862.414
write_gctx0.3880.0340.423
write_gctx_meta0.0000.0010.000
write_gmt0.0000.0010.000
write_grp0.0000.0000.001
write_tbl0.0000.0000.001