Back to Multiple platform build/check report for BioC 3.7
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for crossmeta on tokay2

This page was generated on 2018-10-17 08:42:27 -0400 (Wed, 17 Oct 2018).

Package 325/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crossmeta 1.6.0
Alex Pickering
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/crossmeta
Branch: RELEASE_3_7
Last Commit: 27a284d
Last Changed Date: 2018-04-30 10:35:42 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: crossmeta
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:crossmeta.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings crossmeta_1.6.0.tar.gz
StartedAt: 2018-10-17 01:23:24 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:25:41 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 136.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: crossmeta.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:crossmeta.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings crossmeta_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/crossmeta.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.6.0'
* 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 whether package 'crossmeta' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpOknbmB/R.INSTALL126056a93641/crossmeta/man/es_meta.Rd:37: file link 'zScores' in package 'GeneMeta' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-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 ... NOTE
Missing or unexported objects:
  'crossmeta::gs.names' 'crossmeta::gslist'
* 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'
Undefined global functions or variables:
  gs.names gslist
* 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
Data with usage in documentation object 'gs.names' but not in code:
  gs.names

Data with usage in documentation object 'gslist' but not in code:
  gslist

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
diff_path 6.35   0.37    6.72
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
diff_path 5.59   0.12    5.72
* 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: 2 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/crossmeta.Rcheck/00check.log'
for details.

Installation output

crossmeta.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/crossmeta_1.6.0.tar.gz && rm -rf crossmeta.buildbin-libdir && mkdir crossmeta.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=crossmeta.buildbin-libdir crossmeta_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL crossmeta_1.6.0.zip && rm crossmeta_1.6.0.tar.gz crossmeta_1.6.0.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  657k  100  657k    0     0  2251k      0 --:--:-- --:--:-- --:--:-- 2308k

install for i386

* installing *source* package 'crossmeta' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'crossmeta'
    finding HTML links ... done
    add_sources                             html  
    contribute                              html  
    diff_expr                               html  
    diff_path                               html  
    es_meta                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpOknbmB/R.INSTALL126056a93641/crossmeta/man/es_meta.Rd:37: file link 'zScores' in package 'GeneMeta' does not exist and so has been treated as a topic
    explore_paths                           html  
    get_raw                                 html  
    gs.names                                html  
    gslist                                  html  
    load_diff                               html  
    load_path                               html  
    load_raw                                html  
    open_raw_illum                          html  
    path_meta                               html  
    setup_prev                              html  
    symbol_annot                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'crossmeta' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'crossmeta' as crossmeta_1.6.0.zip
* DONE (crossmeta)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'crossmeta' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

crossmeta.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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")
AnnotatingAnnotatingAnnotatingGSE1_FOO-VEH (# p < 0.05): 3 

GSE1_FOO-VEH (# p < 0.05): 3 

GSE1_FOO-VEH (# p < 0.05): 3 

== testthat results  ===========================================================
OK: 14 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   8.65    0.37    9.01

crossmeta.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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")
AnnotatingAnnotatingAnnotatingGSE1_FOO-VEH (# p < 0.05): 3 

GSE1_FOO-VEH (# p < 0.05): 3 

GSE1_FOO-VEH (# p < 0.05): 3 

== testthat results  ===========================================================
OK: 14 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   7.75    0.34    8.09

Example timings

crossmeta.Rcheck/examples_i386/crossmeta-Ex.timings

nameusersystemelapsed
add_sources0.190.000.19
contribute0.560.050.61
diff_expr0.370.030.40
diff_path6.350.376.72
es_meta3.010.153.16
explore_paths2.330.012.34
get_raw0.210.030.74
load_diff0.230.000.23
load_path0.020.000.02
load_raw0.390.000.39
open_raw_illum0.000.020.01
path_meta000
setup_prev1.230.041.28
symbol_annot3.300.073.36

crossmeta.Rcheck/examples_x64/crossmeta-Ex.timings

nameusersystemelapsed
add_sources0.140.000.14
contribute0.470.000.47
diff_expr0.310.000.32
diff_path5.590.125.72
es_meta2.890.102.99
explore_paths1.970.001.96
get_raw0.090.030.61
load_diff0.220.050.27
load_path000
load_raw0.330.010.34
open_raw_illum0.010.000.02
path_meta000
setup_prev1.110.021.13
symbol_annot3.810.083.89