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

This page was generated on 2022-01-19 13:06:23 -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 tokay2


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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cmapR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cmapR_1.6.0.tar.gz
StartedAt: 2022-01-18 17:23:28 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 17:27:32 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 244.4 seconds
RetCode: 0
Status:   OK  
CheckDir: cmapR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cmapR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cmapR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/cmapR.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'cmapR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/cmapR.Rcheck/00check.log'
for details.



Installation output

cmapR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/cmapR_1.6.0.tar.gz && rm -rf cmapR.buildbin-libdir && mkdir cmapR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cmapR.buildbin-libdir cmapR_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL cmapR_1.6.0.zip && rm cmapR_1.6.0.tar.gz cmapR_1.6.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 11 3557k   11  411k    0     0  1419k      0  0:00:02 --:--:--  0:00:02 1422k
100 3557k  100 3557k    0     0  2864k      0  0:00:01  0:00:01 --:--:-- 2866k

install for i386

* 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
  converting help for package 'cmapR'
    finding HTML links ... done
    GCT-class                               html  
    GCT                                     html  
    align_matrices                          html  
    annotate_gct                            html  
    append_dim                              html  
    cdesc_char                              html  
    check_colnames                          html  
    check_dups                              html  
    distil                                  html  
    ds                                      html  
    extract_gct                             html  
    fix_datatypes                           html  
    gene_set                                html  
    ids                                     html  
    is.wholenumber                          html  
    kd_gct                                  html  
    lxb2mat                                 html  
    mat                                     html  
    melt_gct                                html  
    finding level-2 HTML links ... done

    merge_gct                               html  
    merge_with_precedence                   html  
    meta                                    html  
    na_pad_matrix                           html  
    parse_gctx                              html  
    parse_gmt                               html  
    parse_gmx                               html  
    parse_grp                               html  
    process_ids                             html  
    rank_gct                                html  
    read_gctx_ids                           html  
    read_gctx_meta                          html  
    robust_zscore                           html  
    subset_gct                              html  
    subset_to_ids                           html  
    threshold                               html  
    transpose_gct                           html  
    update_gctx                             html  
    write_gct                               html  
    write_gctx                              html  
    write_gctx_meta                         html  
    write_gmt                               html  
    write_grp                               html  
    write_tbl                               html  
** 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

install for x64

* installing *source* package 'cmapR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cmapR' as cmapR_1.6.0.zip
* DONE (cmapR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'cmapR' successfully unpacked and MD5 sums checked

Tests output

cmapR.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  14.10    1.56   15.51 

cmapR.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  14.37    0.81   15.07 

Example timings

cmapR.Rcheck/examples_i386/cmapR-Ex.timings

nameusersystemelapsed
GCT0.280.140.52
align_matrices000
annotate_gct0.170.010.19
append_dim000
check_colnames000
check_dups000
distil000
extract_gct0.090.000.09
fix_datatypes0.050.000.05
ids0.030.000.03
is.wholenumber000
lxb2mat0.240.050.84
mat000
melt_gct2.180.112.17
merge_gct0.30.00.3
merge_with_precedence0.020.000.02
meta000
na_pad_matrix000
parse_gctx0.250.000.25
parse_gmt0.060.000.07
parse_gmx0.050.000.05
parse_grp0.010.000.02
process_ids0.020.000.01
rank_gct0.250.000.25
read_gctx_ids000
read_gctx_meta0.180.000.19
robust_zscore000
subset_gct0.520.000.52
threshold000
transpose_gct0.090.000.09
update_gctx000
write_gct1.410.161.56
write_gctx0.200.060.27
write_gctx_meta000
write_gmt000
write_grp000
write_tbl000

cmapR.Rcheck/examples_x64/cmapR-Ex.timings

nameusersystemelapsed
GCT0.190.040.22
align_matrices000
annotate_gct0.140.040.19
append_dim000
check_colnames000
check_dups000
distil000
extract_gct0.060.030.09
fix_datatypes0.020.000.01
ids0.030.000.03
is.wholenumber000
lxb2mat0.680.030.72
mat000
melt_gct2.430.132.46
merge_gct0.310.000.31
merge_with_precedence0.010.000.01
meta000
na_pad_matrix0.000.020.02
parse_gctx0.410.000.41
parse_gmt0.050.000.04
parse_gmx0.030.000.03
parse_grp000
process_ids0.010.000.02
rank_gct0.150.000.14
read_gctx_ids0.010.000.02
read_gctx_meta0.140.000.14
robust_zscore000
subset_gct0.050.000.04
threshold000
transpose_gct0.090.000.10
update_gctx000
write_gct1.140.211.36
write_gctx0.240.050.28
write_gctx_meta000
write_gmt000
write_grp000
write_tbl000