Multiple platform build/check report for BioC 3.14 - CHECK results for sparrow on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (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*

Package: sparrow

Version: 1.0.3

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sparrow.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings sparrow_1.0.3.tar.gz

StartedAt: 2022-04-13 03:16:58 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 03:45:10 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 1691.9 seconds

RetCode: 0

Status: OK

CheckDir: sparrow.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sparrow.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings sparrow_1.0.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/sparrow.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 'sparrow/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sparrow' version '1.0.3'
* 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 'sparrow' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
geneSetsStats: no visible binding for global variable 'direction'
Undefined global functions or variables:
  direction
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
goseq                     9.39   0.56    9.73
seas                      6.44   0.81    7.09
geneSetsStats             5.93   0.85    6.52
geneSetSummaryByGenes     5.97   0.31    6.09
annotateGeneSetMembership 5.52   0.55    5.93
scoreSingleSamples        5.33   0.22    5.56
SparrowResult-utilities   5.11   0.35    5.61
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
goseq                     10.02   0.27   10.19
seas                       6.38   0.25    6.51
geneSetsStats              5.78   0.36    6.00
annotateGeneSetMembership  5.33   0.25    5.44
SparrowResult-utilities    5.19   0.25    5.33
scoreSingleSamples         5.23   0.19    5.41
* 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/sparrow.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/sparrow_1.0.3.tar.gz && rm -rf sparrow.buildbin-libdir && mkdir sparrow.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sparrow.buildbin-libdir sparrow_1.0.3.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL sparrow_1.0.3.zip && rm sparrow_1.0.3.tar.gz sparrow_1.0.3.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 29 3013k   29  892k    0     0  1587k      0  0:00:01 --:--:--  0:00:01 1587k
100 3013k  100 3013k    0     0  2303k      0  0:00:01  0:00:01 --:--:-- 2305k

install for i386

* installing *source* package 'sparrow' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sparrow'
    finding HTML links ... done
    GeneSetDb-class                         html  
    SparrowResult-utilities                 html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/sparrow.buildbin-libdir/00LOCK-sparrow/00new/sparrow/help/geneSetDb.html
    SparrowResult                           html  
    addGeneSetMetadata                      html  
    all.equal.GeneSetDb                     html  
    annotateGeneSetMembership               html  
    calculateIndividualLogFC                html  
    collectionMetadata                      html  
    combine-GeneSetDb-GeneSetDb-method      html  
    combine-SparrowResult-SparrowResult-method
                                            html  
    conform                                 html  
    conversion                              html  
    convertIdentifiers                      html  
    corplot                                 html  
    eigenWeightedMean                       html  
    examples                                html  
    failWith                                html  
    featureIdMap                            html  
    featureIds                              html  
    geneSet                                 html  
    geneSetCollectionURLfunction            html  
    geneSetSummaryByGenes                   html  
    geneSets                                html  
    geneSetsStats                           html  
    getKeggCollection                       html  
    getMSigCollection                       html  
    getPantherCollection                    html  
    getReactomeCollection                   html  
    goseq                                   html  
    gsdScore                                html  
    gskey                                   html  
    hasGeneSet                              html  
    hasGeneSetCollection                    html  
    incidenceMatrix                         html  
    iplot                                   html  
    is.active                               html  
    logFC                                   html  
    mgheatmap                               html  
    mgheatmap2                              html  
    msg                                     html  
    ora                                     html  
    p.matrix                                html  
    randomGeneSetDb                         html  
    renameCollections                       html  
    renameRows                              html  
    results                                 html  
    scale_rows                              html  
    scoreSingleSamples                      html  
    seas                                    html  
    finding level-2 HTML links ... done

    sparrow_methods                         html  
    species_info                            html  
    ssGSEA.normalize                        html  
    sub-GeneSetDb-ANY-ANY-ANY-method        html  
    subset.GeneSetDb                        html  
    subsetByFeatures                        html  
    validateInputs                          html  
    volcanoPlot                             html  
    volcanoStatsTable                       html  
    zScore                                  html  
*** copying figures
** 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 'sparrow' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sparrow' as sparrow_1.0.3.zip
* DONE (sparrow)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'sparrow' successfully unpacked and MD5 sums checked


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("sparrow")
> library("testthat")
> library("data.table")
> library("dplyr")

Attaching package: 'dplyr'

The following objects are masked from 'package:data.table':

    between, first, last

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

    matches

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

    combine

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

    filter, lag

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

    intersect, setdiff, setequal, union

> 
> test_check("sparrow")

Attaching package: 'magrittr'

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

    equals, is_less_than, not

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1519 ]

== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1519 ]
> 
> ## Remove temporary files that were generated
> test.dir <- system.file('tests', package = "sparrow")
> pdfs <- dir(test.dir, "\\.pdf$", full.names=TRUE)
> if (length(pdfs)) {
+   unlink(pdfs)
+ }
> 
> 
> proc.time()
   user  system elapsed 
 434.95   31.43  635.07


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("sparrow")
> library("testthat")
> library("data.table")
> library("dplyr")

Attaching package: 'dplyr'

The following objects are masked from 'package:data.table':

    between, first, last

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

    matches

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

    combine

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

    filter, lag

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

    intersect, setdiff, setequal, union

> 
> test_check("sparrow")

Attaching package: 'magrittr'

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

    equals, is_less_than, not

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1483 ]

== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1483 ]
> 
> ## Remove temporary files that were generated
> test.dir <- system.file('tests', package = "sparrow")
> pdfs <- dir(test.dir, "\\.pdf$", full.names=TRUE)
> if (length(pdfs)) {
+   unlink(pdfs)
+ }
> 
> 
> proc.time()
   user  system elapsed 
 462.21   19.53  657.17

name	user	system	elapsed
GeneSetDb-class	0.06	0.00	0.06
SparrowResult-utilities	5.11	0.35	5.61
addGeneSetMetadata	0.15	0.01	0.16
annotateGeneSetMembership	5.52	0.55	5.93
calculateIndividualLogFC	2.45	0.05	2.50
collectionMetadata	0.08	0.01	0.10
combine-GeneSetDb-GeneSetDb-method	0.09	0.02	0.11
combine-SparrowResult-SparrowResult-method	0.24	0.01	0.45
conform	0.62	0.00	0.61
conversion	1.25	0.04	1.28
convertIdentifiers	0.27	0.03	0.28
corplot	0.15	0.00	0.16
eigenWeightedMean	2.54	0.00	2.53
examples	0.40	0.03	0.44
failWith	0	0	0
featureIdMap	0.75	0.03	0.78
featureIds	0.69	0.00	0.68
geneSet	0.09	0.00	0.10
geneSetCollectionURLfunction	0.10	0.00	0.08
geneSetSummaryByGenes	5.97	0.31	6.09
geneSets	0.07	0.03	0.09
geneSetsStats	5.93	0.85	6.52
getKeggCollection	0	0	0
getMSigCollection	0	0	0
getPantherCollection	0	0	0
getReactomeCollection	0	0	0
goseq	9.39	0.56	9.73
gsdScore	1.32	0.01	1.33
gskey	0	0	0
hasGeneSet	0.07	0.02	0.08
hasGeneSetCollection	0.07	0.02	0.08
incidenceMatrix	1.18	0.00	1.17
iplot	1.12	0.06	1.19
is.active	0.63	0.33	1.79
logFC	4.14	0.31	4.36
mgheatmap	0	0	0
mgheatmap2	0	0	0
msg	0	0	0
ora	0.48	0.34	1.55
p.matrix	0.13	0.00	0.13
randomGeneSetDb	1.17	0.28	2.15
renameCollections	0.09	0.04	0.11
renameRows	0.42	0.03	0.45
results	0.14	0.01	0.16
scale_rows	0	0	0
scoreSingleSamples	5.33	0.22	5.56
seas	6.44	0.81	7.09
sparrow_methods	0	0	0
species_info	0.01	0.00	0.02
subset.GeneSetDb	0.10	0.03	0.14
subsetByFeatures	0.10	0.10	0.19
validateInputs	0.35	0.34	1.37
volcanoPlot	2.30	0.11	2.41
volcanoStatsTable	0.07	0.03	0.11
zScore	0.91	0.07	0.97

name	user	system	elapsed
GeneSetDb-class	0.09	0.02	0.11
SparrowResult-utilities	5.19	0.25	5.33
addGeneSetMetadata	0.08	0.00	0.08
annotateGeneSetMembership	5.33	0.25	5.44
calculateIndividualLogFC	2.39	0.03	2.42
collectionMetadata	0.09	0.00	0.09
combine-GeneSetDb-GeneSetDb-method	0.17	0.02	0.14
combine-SparrowResult-SparrowResult-method	0.21	0.01	0.22
conform	0.48	0.03	0.52
conversion	0.63	0.05	0.67
convertIdentifiers	0.22	0.05	0.25
corplot	0.14	0.01	0.16
eigenWeightedMean	2.26	0.02	2.26
examples	0.39	0.03	0.42
failWith	0.02	0.00	0.02
featureIdMap	0.45	0.05	0.48
featureIds	1.17	0.01	1.21
geneSet	0.10	0.00	0.07
geneSetCollectionURLfunction	0.06	0.00	0.07
geneSetSummaryByGenes	3.52	0.11	3.59
geneSets	0.07	0.00	0.08
geneSetsStats	5.78	0.36	6.00
getKeggCollection	0	0	0
getMSigCollection	0	0	0
getPantherCollection	0	0	0
getReactomeCollection	0	0	0
goseq	10.02	0.27	10.19
gsdScore	1.17	0.00	1.17
gskey	0	0	0
hasGeneSet	0.08	0.00	0.08
hasGeneSetCollection	0.11	0.00	0.10
incidenceMatrix	1.56	0.02	1.57
iplot	1.11	0.08	1.32
is.active	0.58	0.35	1.64
logFC	4.23	0.18	4.31
mgheatmap	0	0	0
mgheatmap2	0.02	0.00	0.01
msg	0	0	0
ora	0.50	0.34	1.57
p.matrix	0.14	0.00	0.14
randomGeneSetDb	0.08	0.31	1.11
renameCollections	0.10	0.00	0.08
renameRows	0.51	0.03	0.55
results	0.13	0.00	0.12
scale_rows	0	0	0
scoreSingleSamples	5.23	0.19	5.41
seas	6.38	0.25	6.51
sparrow_methods	0	0	0
species_info	0.02	0.00	0.02
subset.GeneSetDb	0.14	0.00	0.14
subsetByFeatures	0.11	0.02	0.12
validateInputs	0.25	0.26	1.20
volcanoPlot	2.51	0.08	2.69
volcanoStatsTable	0.11	0.00	0.11
zScore	0.99	0.03	1.02

CHECK results for sparrow on tokay2

Summary

Command output

Installation output

Tests output

Example timings