Back to Multiple platform build/check report for BioC 3.9
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for crossmeta on malbec2

This page was generated on 2019-10-16 12:09:08 -0400 (Wed, 16 Oct 2019).

Package 367/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crossmeta 1.10.0
Alex Pickering
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/crossmeta
Branch: RELEASE_3_9
Last Commit: 4f66dee
Last Changed Date: 2019-05-02 11:54:02 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
##############################################################################
###
### Running 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
###
##############################################################################
##############################################################################


* 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.



Installation output

crossmeta.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL crossmeta
###
##############################################################################
##############################################################################


* 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)

Tests output

crossmeta.Rcheck/tests/testthat.Rout


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 

Example timings

crossmeta.Rcheck/crossmeta-Ex.timings

nameusersystemelapsed
add_sources0.2520.0000.252
contribute0.8170.0120.829
diff_expr0.5280.0160.580
diff_path7.1030.1367.365
es_meta4.0470.0484.095
explore_paths3.2310.0043.235
get_raw0.8400.0631.823
load_diff0.2650.0040.269
load_path0.0120.0030.014
load_raw0.3620.0040.365
path_meta0.0140.0000.013
setup_prev1.3960.0441.440
symbol_annot8.2410.0885.625