BioC 3.5: CHECK report for crossmeta on tokay2

Package: crossmeta

Version: 1.2.0

Command: rm -rf crossmeta.buildbin-libdir crossmeta.Rcheck && mkdir crossmeta.buildbin-libdir crossmeta.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=crossmeta.buildbin-libdir crossmeta_1.2.0.tar.gz >crossmeta.Rcheck\00install.out 2>&1 && cp crossmeta.Rcheck\00install.out crossmeta-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=crossmeta.buildbin-libdir --install="check:crossmeta-install.out" --force-multiarch --no-vignettes --timings crossmeta_1.2.0.tar.gz

StartedAt: 2017-10-17 23:05:29 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 23:08:02 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 153.4 seconds

RetCode: 1

Status:  ERROR

CheckDir: crossmeta.Rcheck

Warnings: NA

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### Running command:
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###   rm -rf crossmeta.buildbin-libdir crossmeta.Rcheck && mkdir crossmeta.buildbin-libdir crossmeta.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=crossmeta.buildbin-libdir crossmeta_1.2.0.tar.gz >crossmeta.Rcheck\00install.out 2>&1 && cp crossmeta.Rcheck\00install.out crossmeta-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=crossmeta.buildbin-libdir --install="check:crossmeta-install.out" --force-multiarch --no-vignettes --timings crossmeta_1.2.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/crossmeta.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.2.0'
* 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 ... 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
* 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 installed files from 'inst/doc' ... 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 8.66   0.31   11.24
** running examples for arch 'x64' ... ERROR
Running examples in 'crossmeta-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_raw
> ### Title: Download and unpack microarray supplementary files from GEO.
> ### Aliases: get_raw
> 
> ### ** Examples
> 
> get_raw("GSE41845")
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE41nnn/GSE41845/suppl/
OK
Error in download.file(file.path(url, i), destfile = file.path(storedir,  : 
  cannot open destfile 'C:/Users/biocbuild/bbs-3.5-bioc/meat/crossmeta.Rcheck/examples_x64/GSE41845//geo/series/GSE41nnn/GSE41845', reason 'No such file or directory'
Calls: get_raw -> <Anonymous> -> download.file
Execution halted
* 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: 1 ERROR, 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/crossmeta.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'crossmeta' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'crossmeta' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'crossmeta' as crossmeta_1.2.0.zip
* DONE (crossmeta)

name	user	system	elapsed
add_sources	0.17	0.00	0.17
contribute	1.00	0.02	1.01
diff_expr	0.83	0.03	1.14
diff_path	8.66	0.31	11.24
es_meta	3.01	0.08	3.09
explore_paths	1.90	0.03	1.92
get_raw	0.62	0.17	1.47
load_diff	0.33	0.00	0.33
load_path	0.01	0.00	0.02
load_raw	0.36	0.00	0.35
open_raw_illum	0.02	0.00	0.02
path_meta	0	0	0
setup_prev	1.12	0.02	1.14
symbol_annot	3.39	0.00	3.39

name	user	system	elapsed
add_sources	0.18	0.02	0.19
contribute	1.43	0.01	1.46
diff_expr	0.8	0.0	0.8
diff_path	9.86	0.17	10.03
es_meta	4.73	0.08	4.81
explore_paths	2.52	0.00	2.52