Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:29 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 easier on tokay2


To the developers/maintainers of the easier package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/easier.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 554/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
easier 1.0.0  (landing page)
Oscar Lapuente-Santana
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/easier
git_branch: RELEASE_3_14
git_last_commit: efb058c
git_last_commit_date: 2021-10-26 13:14:15 -0400 (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: easier
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:easier.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings easier_1.0.0.tar.gz
StartedAt: 2022-04-12 18:58:04 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 19:21:11 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 1387.6 seconds
RetCode: 0
Status:   OK  
CheckDir: easier.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:easier.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings easier_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/easier.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'easier/DESCRIPTION' ... OK
* this is package 'easier' version '1.0.0'
* package encoding: UTF-8
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'easier' can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
Namespace in Imports field not imported from: 'coin'
  All declared Imports should be used.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
compute_cell_fractions         70.66   2.13   76.07
assess_immune_response         40.79   4.29   74.47
explore_biomarkers             34.88   0.83   41.03
predict_immune_response        27.45   1.49   39.57
retrieve_easier_score          26.66   1.68   30.62
compute_CC_pairs               25.54   1.08   96.70
compute_CCpair_score           24.77   1.20   29.24
compute_LR_pairs               16.22   0.74   56.32
compute_pathway_activity       15.91   0.48   19.20
compute_TF_activity            14.25   0.65   16.13
compute_scores_immune_response  9.68   0.39   11.03
categorize_TMB                  5.13   0.22    5.80
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
compute_cell_fractions         59.60   0.32   60.33
assess_immune_response         38.44   2.42   99.31
explore_biomarkers             34.45   0.77   65.24
retrieve_easier_score          29.19   1.23   35.05
predict_immune_response        29.14   0.92   39.63
compute_CC_pairs               26.45   0.88   29.42
compute_CCpair_score           26.08   0.86   28.93
compute_LR_pairs               16.49   0.64   18.41
compute_pathway_activity       16.34   0.31   17.63
compute_TF_activity            14.18   0.59   16.01
compute_scores_immune_response 10.11   0.37   11.46
categorize_TMB                  5.34   0.26    5.95
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/easier.Rcheck/00check.log'
for details.

Installation output

easier.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/easier_1.0.0.tar.gz && rm -rf easier.buildbin-libdir && mkdir easier.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=easier.buildbin-libdir easier_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL easier_1.0.0.zip && rm easier_1.0.0.tar.gz easier_1.0.0.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
 86  829k   86  716k    0     0  1272k      0 --:--:-- --:--:-- --:--:-- 1271k
100  829k  100  829k    0     0   883k      0 --:--:-- --:--:-- --:--:--  883k

install for i386

* installing *source* package 'easier' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'easier'
    finding HTML links ... done
    assess_immune_response                  html  
    calc_z_score                            html  
    categorize_TMB                          html  
    compute_Ayers_expIS                     html  
    compute_CC_pairs                        html  
    compute_CCpair_score                    html  
    compute_CYT                             html  
    compute_Davoli_IS                       html  
    compute_IFNy                            html  
    compute_IMPRES_MSI                      html  
    compute_LR_pairs                        html  
    compute_RIR                             html  
    compute_Roh_IS                          html  
    compute_TF_activity                     html  
    compute_TLS                             html  
    compute_Tcell_inflamed                  html  
    compute_cell_fractions                  html  
    compute_chemokines                      html  
    compute_pathway_activity                html  
    compute_scores_immune_response          html  
    easier-pkg                              html  
    explore_biomarkers                      html  
    get_OE_bulk                             html  
    get_semi_random_OE                      html  
    predict_immune_response                 html  
    predict_with_rmtlr                      html  
    reannotate_genes                        html  
    retrieve_easier_score                   html  
    rmtlr_test                              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 'easier' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'easier' as easier_1.0.0.zip
* DONE (easier)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'easier' successfully unpacked and MD5 sums checked

Tests output

easier.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(easier)
> 
> test_check("easier")
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

snapshotDate(): 2021-10-19
Retrieving Mariathasan2018_PDL1_treatment dataset...
see ?easierData and browseVignettes('easierData') for documentation
loading from cache
Regulated transcripts found in data set: 3084/3254 (94.8%)
TF activity computed! 

Computing predictions using tfs...

snapshotDate(): 2021-10-19
Retrieving Mariathasan2018_PDL1_treatment dataset...
see ?easierData and browseVignettes('easierData') for documentation
loading from cache
Regulated transcripts found in data set: 3084/3254 (94.8%)
TF activity computed! 

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
  58.57    5.51   68.34

easier.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(easier)
> 
> test_check("easier")
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

snapshotDate(): 2021-10-19
Retrieving Mariathasan2018_PDL1_treatment dataset...
see ?easierData and browseVignettes('easierData') for documentation
loading from cache
Regulated transcripts found in data set: 3084/3254 (94.8%)
TF activity computed! 

Computing predictions using tfs...

snapshotDate(): 2021-10-19
Retrieving Mariathasan2018_PDL1_treatment dataset...
see ?easierData and browseVignettes('easierData') for documentation
loading from cache
Regulated transcripts found in data set: 3084/3254 (94.8%)
TF activity computed! 

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
  62.10    3.37   69.64

Example timings

easier.Rcheck/examples_i386/easier-Ex.timings

nameusersystemelapsed
assess_immune_response40.79 4.2974.47
calc_z_score000
categorize_TMB5.130.225.80
compute_CC_pairs25.54 1.0896.70
compute_CCpair_score24.77 1.2029.24
compute_LR_pairs16.22 0.7456.32
compute_TF_activity14.25 0.6516.13
compute_cell_fractions70.66 2.1376.07
compute_pathway_activity15.91 0.4819.20
compute_scores_immune_response 9.68 0.3911.03
explore_biomarkers34.88 0.8341.03
get_OE_bulk000
get_semi_random_OE000
predict_immune_response27.45 1.4939.57
predict_with_rmtlr000
reannotate_genes000
retrieve_easier_score26.66 1.6830.62
rmtlr_test000

easier.Rcheck/examples_x64/easier-Ex.timings

nameusersystemelapsed
assess_immune_response38.44 2.4299.31
calc_z_score000
categorize_TMB5.340.265.95
compute_CC_pairs26.45 0.8829.42
compute_CCpair_score26.08 0.8628.93
compute_LR_pairs16.49 0.6418.41
compute_TF_activity14.18 0.5916.01
compute_cell_fractions59.60 0.3260.33
compute_pathway_activity16.34 0.3117.63
compute_scores_immune_response10.11 0.3711.46
explore_biomarkers34.45 0.7765.24
get_OE_bulk000
get_semi_random_OE000
predict_immune_response29.14 0.9239.63
predict_with_rmtlr000
reannotate_genes000
retrieve_easier_score29.19 1.2335.05
rmtlr_test000