Package: crossmeta

Version: 1.12.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:crossmeta.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings crossmeta_1.12.0.tar.gz

StartedAt: 2020-04-15 02:23:57 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:26:39 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 162.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: crossmeta.Rcheck

Warnings: 2

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:crossmeta.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings crossmeta_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/crossmeta.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.12.0'
* 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-3.10-bioc/tmpdir/RtmpYXXtvS/R.INSTALL28cc55285f1d/crossmeta/man/es_meta.Rd:38: file link 'zScores' in package 'GeneMeta' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-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: 'shinyBS'
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
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_dfs: no visible global function definition for 'head'
load_agil_plat : <anonymous>: 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'
which_max_iqr: no visible binding for global variable 'iqrange'
Undefined global functions or variables:
  SYMBOL_9606 as capture.output download.file head iqrange is
  read.table
Consider adding
  importFrom("methods", "as", "is")
  importFrom("utils", "capture.output", "download.file", "head",
             "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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
diff_path 8.57   0.34   12.73
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
diff_path 8.11   0.17    8.28
* 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/crossmeta.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/crossmeta_1.12.0.tar.gz && rm -rf crossmeta.buildbin-libdir && mkdir crossmeta.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=crossmeta.buildbin-libdir crossmeta_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL crossmeta_1.12.0.zip && rm crossmeta_1.12.0.tar.gz crossmeta_1.12.0.zip
###
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  % 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 2724k  100 2724k    0     0  26.8M      0 --:--:-- --:--:-- --:--:-- 28.0M

install for i386

* 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
  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-3.10-bioc/tmpdir/RtmpYXXtvS/R.INSTALL28cc55285f1d/crossmeta/man/es_meta.Rd:38: file link 'zScores' in package 'GeneMeta' does not exist and so has been treated as a topic
    explore_paths                           html  
    format_fdrs                             html  
    get_raw                                 html  
    gs.names                                html  
    gslist                                  html  
    load_diff                               html  
    load_path                               html  
    load_raw                                html  
    path_meta                               html  
    setup_prev                              html  
    symbol_annot                            html  
    which_max_iqr                           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_1.12.0.zip
* DONE (crossmeta)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'crossmeta' successfully unpacked and MD5 sums checked

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.
== testthat results  ===========================================================
[ OK: 15 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   4.95    0.48    5.40 

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.
== testthat results  ===========================================================
[ OK: 15 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   8.43    0.37    8.81