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CHECK report for crossmeta on tokay1

This page was generated on 2021-05-05 12:11:37 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the crossmeta package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 400/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crossmeta 1.16.1  (landing page)
Alex Pickering
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/crossmeta
Branch: RELEASE_3_12
Last Commit: 02d63d6
Last Changed Date: 2020-11-02 13:21:38 -0400 (Mon, 02 Nov 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: crossmeta
Version: 1.16.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:crossmeta.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings crossmeta_1.16.1.tar.gz
StartedAt: 2021-05-05 01:54:47 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 01:57:35 -0400 (Wed, 05 May 2021)
EllapsedTime: 168.0 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: crossmeta.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:crossmeta.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings crossmeta_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/crossmeta.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'crossmeta/DESCRIPTION' ... OK
* this is package 'crossmeta' version '1.16.1'
* 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 'crossmeta' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpQDdHXU/R.INSTALL19041bb6acc/crossmeta/man/es_meta.Rd:38: file link 'zScores' in package 'GeneMeta' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpQDdHXU/R.INSTALL19041bb6acc/crossmeta/man/exprs.MA.Rd:17: file link 'plotDensities.MAList' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpQDdHXU/R.INSTALL19041bb6acc/crossmeta/man/exprs.MA.Rd:17: file link 'exprs.MA' in package 'limma' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/crossmeta.Rcheck/00install.out' for details.
* 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 ... WARNING
'::' or ':::' import not declared from: 'tibble'
Namespace in Imports field not imported from: 'statmod'
  All declared Imports should be used.
Unexported object imported by a ':::' call: 'GEOquery:::parseGSEMatrix'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'getDirListing' 'getGEO' 'getGEOSuppFiles'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
add_contrasts: no visible global function definition for
  'select_contrasts'
bulkAnnot : <anonymous>: no visible global function definition for
  'write.csv'
bulkAnnot: no visible global function definition for 'html'
bulkAnnot: no visible global function definition for 'toggleClass'
bulkAnnot: no visible global function definition for 'read.csv'
diff_anal: no visible global function definition for 'model.matrix'
getAndParseGSEMatrices: no visible global function definition for
  'download.file'
getDirListing: no visible global function definition for 'read.table'
getGEOSuppFiles: no visible global function definition for
  'download.file'
get_palette: no visible global function definition for 'head'
is_invertible: no visible global function definition for 'is'
load_agil_plat : <anonymous>: no visible global function definition for
  'capture.output'
load_raw: no visible global function definition for 'setNames'
symbol_annot: no visible binding for global variable 'SYMBOL_9606'
to_eset: no visible global function definition for 'as'
to_ma: no visible global function definition for 'new'
which_max_iqr: no visible binding for global variable 'iqrange'
xls_to_txt: no visible global function definition for 'write.table'
Undefined global functions or variables:
  SYMBOL_9606 as capture.output download.file head html iqrange is
  model.matrix new read.csv read.table select_contrasts setNames
  toggleClass write.csv write.table
Consider adding
  importFrom("methods", "as", "is", "new")
  importFrom("stats", "model.matrix", "setNames")
  importFrom("utils", "capture.output", "download.file", "head",
             "read.csv", "read.table", "write.csv", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'add_sources':
add_sources
  Code: function(diff_exprs, data_dir = getwd(), postfix = NULL)
  Docs: function(diff_exprs, data_dir = getwd())
  Argument names in code not in docs:
    postfix

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'ch2_subset'
  'prev_anal'

Undocumented arguments in documentation object 'get_sva_mods'
  'pdata'
Documented arguments not in \usage in documentation object 'get_sva_mods':
  'eset'

Undocumented arguments in documentation object 'iqr_replicates'
  'eset'
Documented arguments not in \usage in documentation object 'iqr_replicates':
  'mod' 'svobj'

Undocumented arguments in documentation object 'run_select_contrasts'
  'port'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
symbol_annot 6.16   0.09    6.44
* 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: 4 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/crossmeta.Rcheck/00check.log'
for details.



Installation output

crossmeta.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/crossmeta_1.16.1.tar.gz && rm -rf crossmeta.buildbin-libdir && mkdir crossmeta.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=crossmeta.buildbin-libdir crossmeta_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL crossmeta_1.16.1.zip && rm crossmeta_1.16.1.tar.gz crossmeta_1.16.1.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
100 3866k  100 3866k    0     0  38.7M      0 --:--:-- --:--:-- --:--:-- 39.3M

install for i386

* installing *source* package 'crossmeta' ...
** 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 'crossmeta'
    finding HTML links ... done
    addContrastInput                        html  
    add_adjusted                            html  
    add_sources                             html  
    bulkAnnot                               html  
    bulkAnnotInput                          html  
    bulkForm                                html  
    bulkFormInput                           html  
    bulkPage                                html  
    bulkPageUI                              html  
    bulkTable                               html  
    bulkTableOuput                          html  
    ch2_subset                              html  
    delContrastsInput                       html  
    diff_expr                               html  
    es_meta                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpQDdHXU/R.INSTALL19041bb6acc/crossmeta/man/es_meta.Rd:38: file link 'zScores' in package 'GeneMeta' does not exist and so has been treated as a topic
    exprs.MA                                html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpQDdHXU/R.INSTALL19041bb6acc/crossmeta/man/exprs.MA.Rd:17: file link 'plotDensities.MAList' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpQDdHXU/R.INSTALL19041bb6acc/crossmeta/man/exprs.MA.Rd:17: file link 'exprs.MA' in package 'limma' does not exist and so has been treated as a topic
    fix_illum_headers                       html  
    finding level-2 HTML links ... done

    format_dl_annot                         html  
    format_up_annot                         html  
    get_ch2_mod                             html  
    get_group_levels                        html  
    get_palette                             html  
    get_raw                                 html  
    get_sva_mods                            html  
    gs.names                                html  
    gslist                                  html  
    ilmn.nnum                               html  
    iqr_replicates                          html  
    is_invertible                           html  
    load_agil_plat                          html  
    load_diff                               html  
    load_raw                                html  
    open_raw_illum                          html  
    phenoData.ch2                           html  
    prefix_illum_headers                    html  
    query_ref                               html  
    run_select_contrasts                    html  
    run_sva                                 html  
    setup_prev                              html  
    symbol_annot                            html  
    to_eset                                 html  
    to_ma                                   html  
    validate_up_annot                       html  
    which_max_iqr                           html  
    xls_to_txt                              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 'crossmeta' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'crossmeta' as crossmeta_1.16.1.zip
* DONE (crossmeta)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'crossmeta' successfully unpacked and MD5 sums checked

Tests output

crossmeta.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(crossmeta)
> 
> test_check("crossmeta")
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by column names.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Apoa1_ApoAI...-C57BL.6 (# p < 0.05): 20 

Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ]
> 
> proc.time()
   user  system elapsed 
  24.09    0.59   25.00 

crossmeta.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(crossmeta)
> 
> test_check("crossmeta")
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by column names.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Illumina samples matched by pdata column.
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Apoa1_ApoAI...-C57BL.6 (# p < 0.05): 20 

Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 7 corrected
Array 8 corrected
Array 9 corrected
Array 10 corrected
Array 11 corrected
Array 12 corrected
Array 13 corrected
Array 14 corrected
Array 15 corrected
Array 16 corrected
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ]
> 
> proc.time()
   user  system elapsed 
  32.85    0.46   33.32 

Example timings

crossmeta.Rcheck/examples_i386/crossmeta-Ex.timings

nameusersystemelapsed
add_sources0.160.040.21
diff_expr0.360.032.50
es_meta2.730.132.86
get_raw0.810.141.06
load_diff0.180.000.18
load_raw0.260.000.26
open_raw_illum0.020.000.02
setup_prev1.430.062.79
symbol_annot4.720.264.97
to_ma000

crossmeta.Rcheck/examples_x64/crossmeta-Ex.timings

nameusersystemelapsed
add_sources0.140.030.17
diff_expr0.320.020.35
es_meta3.370.073.46
get_raw0.890.081.03
load_diff0.160.000.15
load_raw0.240.000.24
open_raw_illum0.010.000.01
setup_prev1.390.021.41
symbol_annot6.160.096.44
to_ma0.010.000.01