Package: crossmeta

Version: 1.10.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:crossmeta.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings crossmeta_1.10.0.tar.gz

StartedAt: 2019-10-16 00:53:00 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:54:43 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 103.0 seconds

RetCode: 0

Status:  OK

CheckDir: crossmeta.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:crossmeta.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings crossmeta_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/crossmeta.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crossmeta/DESCRIPTION’ ... OK
* this is package ‘crossmeta’ version ‘1.10.0’
* 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 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 ... NOTE
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’ ‘merge_fdata’
  ‘symbol_annot’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
explore_paths : server: no visible binding for global variable ‘gslist’
explore_paths : server: no visible binding for global variable
  ‘gs.names’
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’
load_agil_plat : : no visible global function definition for
  ‘capture.output’
load_agil_plat: no visible global function definition for ‘as’
load_illum_plat: no visible global function definition for ‘as’
padog: no visible global function definition for ‘is’
symbol_annot: no visible binding for global variable ‘SYMBOL_9606’
Undefined global functions or variables:
  SYMBOL_9606 as capture.output download.file gs.names gslist is
  read.table
Consider adding
  importFrom("methods", "as", "is")
  importFrom("utils", "capture.output", "download.file", "read.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 ... 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
symbol_annot 8.241  0.088   5.625
diff_path    7.103  0.136   7.365
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/crossmeta.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL crossmeta
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘crossmeta’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 13 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  5.614   0.230   5.830 

name	user	system	elapsed
add_sources	0.252	0.000	0.252
contribute	0.817	0.012	0.829
diff_expr	0.528	0.016	0.580
diff_path	7.103	0.136	7.365
es_meta	4.047	0.048	4.095
explore_paths	3.231	0.004	3.235
get_raw	0.840	0.063	1.823
load_diff	0.265	0.004	0.269
load_path	0.012	0.003	0.014
load_raw	0.362	0.004	0.365
path_meta	0.014	0.000	0.013
setup_prev	1.396	0.044	1.440
symbol_annot	8.241	0.088	5.625