Multiple platform build/check report for BioC 3.18 - CHECK results for cmapR on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4667
palomino4	Windows Server 2022 Datacenter	x64	4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"	4403
merida1	macOS 12.7.1 Monterey	x86_64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4426
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*

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:cmapR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings cmapR_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/cmapR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘1.14.0’
* 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘tutorial.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/cmapR.Rcheck/00check.log’
for details.

Installation output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL cmapR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-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


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.
[ 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 
 15.123   1.070  15.964

Example timings

name	user	system	elapsed
GCT	0.162	0.011	0.175
align_matrices	0.002	0.000	0.002
annotate_gct	0.144	0.020	0.163
append_dim	0	0	0
check_colnames	0.000	0.002	0.002
check_dups	0	0	0
distil	0.000	0.002	0.001
extract_gct	0.056	0.007	0.063
fix_datatypes	0.006	0.003	0.010
ids	0.013	0.009	0.022
is.wholenumber	0	0	0
lxb2mat	0.658	0.007	0.666
mat	0.000	0.001	0.001
melt_gct	1.559	0.058	1.446
merge_gct	0.063	0.000	0.063
merge_with_precedence	0.006	0.000	0.006
meta	0.002	0.000	0.002
na_pad_matrix	0.002	0.000	0.001
parse_gctx	0.168	0.000	0.168
parse_gmt	0.014	0.004	0.018
parse_gmx	0.009	0.000	0.009
parse_grp	0.002	0.000	0.001
process_ids	0.005	0.000	0.005
rank_gct	0.079	0.000	0.080
read_gctx_ids	0.007	0.000	0.007
read_gctx_meta	0.097	0.004	0.100
robust_zscore	0.000	0.000	0.001
subset_gct	0.038	0.000	0.039
threshold	0	0	0
transpose_gct	0.022	0.004	0.025
update_gctx	0	0	0
write_gct	0.903	0.032	0.935
write_gctx	0.187	0.008	0.196
write_gctx_meta	0	0	0
write_gmt	0	0	0
write_grp	0	0	0
write_tbl	0	0	0

CHECK results for cmapR on nebbiolo2

Summary

Command output

Installation output

Tests output

Example timings