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This page was generated on 2024-06-13 12:18 -0400 (Thu, 13 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4344
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

Package 375/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cmapR 1.17.0  (landing page)
Ted Natoli
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/cmapR
git_branch: devel
git_last_commit: f48edb8
git_last_commit_date: 2024-04-30 11:21:56 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for cmapR on nebbiolo2

To the developers/maintainers of the cmapR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: cmapR
Version: 1.17.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:cmapR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings cmapR_1.17.0.tar.gz
StartedAt: 2024-06-12 21:44:58 -0400 (Wed, 12 Jun 2024)
EndedAt: 2024-06-12 21:48:18 -0400 (Wed, 12 Jun 2024)
EllapsedTime: 199.4 seconds
RetCode: 0
Status:   OK  
CheckDir: cmapR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:cmapR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings cmapR_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/cmapR.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘cmapR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cmapR’ version ‘1.17.0’
* 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      2.2Mb
    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 code 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 loading without being on the library search path ... 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
aggregate_gct: no visible binding for global variable ‘.SD’
Undefined global functions or variables:
  .SD
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/cmapR.Rcheck/00check.log’
for details.


Installation output

cmapR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL cmapR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 168 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test_0.2_io.R:66:1', 'test_0.2_io.R:115:1'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 168 ]
> 
> proc.time()
   user  system elapsed 
 14.968   0.833  15.582 

Example timings

cmapR.Rcheck/cmapR-Ex.timings

nameusersystemelapsed
GCT0.1570.0120.170
align_matrices0.0030.0000.003
annotate_gct0.1470.0000.148
append_dim0.0000.0000.001
check_colnames0.0020.0000.003
check_dups0.0000.0000.001
distil0.0010.0000.001
extract_gct0.6050.0160.620
fix_datatypes0.0090.0000.009
ids0.0130.0040.017
is.wholenumber000
lxb2mat0.1030.0070.110
mat0.0000.0010.001
melt_gct2.0800.1262.044
merge_gct0.060.000.06
merge_with_precedence0.0060.0000.006
meta0.0020.0000.002
na_pad_matrix0.0020.0000.002
parse_gctx0.1610.0160.177
parse_gmt0.0210.0000.021
parse_gmx0.0070.0030.011
parse_grp0.0020.0010.002
process_ids0.0020.0030.005
rank_gct0.0790.0110.091
read_gctx_ids0.0090.0010.008
read_gctx_meta0.0970.0160.113
robust_zscore0.0010.0000.001
subset_gct0.0330.0040.037
threshold000
transpose_gct0.0180.0070.025
update_gctx000
write_gct0.9780.0311.011
write_gctx0.2020.0210.222
write_gctx_meta0.0000.0000.001
write_gmt000
write_grp000
write_tbl000