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CHECK report for crossmeta on merida1

This page was generated on 2021-05-05 12:14:02 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:crossmeta.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings crossmeta_1.16.1.tar.gz
StartedAt: 2021-05-05 01:17:43 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 01:19:58 -0400 (Wed, 05 May 2021)
EllapsedTime: 135.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: crossmeta.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:crossmeta.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings crossmeta_1.16.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/crossmeta.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘crossmeta’ 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
symbol_annot 5.317  0.136   5.459
get_raw      1.272  0.058   6.970
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/crossmeta.Rcheck/00check.log’
for details.



Installation output

crossmeta.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL crossmeta
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* 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
** 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 (crossmeta)

Tests output

crossmeta.Rcheck/tests/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-apple-darwin17.0 (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 
 32.872   0.746  33.643 

Example timings

crossmeta.Rcheck/crossmeta-Ex.timings

nameusersystemelapsed
add_sources0.2110.0070.219
diff_expr0.4360.0200.458
es_meta3.8170.1413.963
get_raw1.2720.0586.970
load_diff0.2120.0050.217
load_raw0.2970.0080.305
open_raw_illum0.0070.0020.008
setup_prev1.5360.0401.579
symbol_annot5.3170.1365.459
to_ma0.010.000.01