BioC 3.5: CHECK report for recount on tokay2

Package: recount

Version: 1.2.3

Command: rm -rf recount.buildbin-libdir recount.Rcheck && mkdir recount.buildbin-libdir recount.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=recount.buildbin-libdir recount_1.2.3.tar.gz >recount.Rcheck\00install.out 2>&1 && cp recount.Rcheck\00install.out recount-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=recount.buildbin-libdir --install="check:recount-install.out" --force-multiarch --no-vignettes --timings recount_1.2.3.tar.gz

StartedAt: 2017-10-18 02:27:25 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:51:46 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 1460.5 seconds

RetCode: 0

Status:  OK

CheckDir: recount.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf recount.buildbin-libdir recount.Rcheck && mkdir recount.buildbin-libdir recount.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=recount.buildbin-libdir recount_1.2.3.tar.gz >recount.Rcheck\00install.out 2>&1 && cp recount.Rcheck\00install.out recount-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=recount.buildbin-libdir --install="check:recount-install.out" --force-multiarch --no-vignettes --timings recount_1.2.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/recount.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 'recount/DESCRIPTION' ... OK
* this is package 'recount' version '1.2.3'
* 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 'recount' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 13.1Mb
  sub-directories of 1Mb or more:
    data  10.7Mb
    doc    2.3Mb
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
add_predictions: no visible binding for global variable
  'PredictedPhenotypes'
Undefined global functions or variables:
  PredictedPhenotypes
* 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 ... NOTE
  Note: found 347 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... 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
reproduce_ranges 126.64   7.75  139.05
snaptron_query     1.37   0.00    7.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
reproduce_ranges    142.80   5.59  152.95
snaptron_query        2.05   0.06    7.80
geo_characteristics   1.67   0.05    5.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/recount.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'recount' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'recount' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'recount' as recount_1.2.3.zip
* DONE (recount)

name	user	system	elapsed
abstract_search	0.87	0.03	0.91
add_predictions	2.49	0.17	3.12
all_metadata	0.93	0.19	1.85
browse_study	0.35	0.00	0.34
coverage_matrix	0	0	0
download_study	1.72	0.11	2.85
expressed_regions	0	0	0
find_geo	0.73	0.03	1.82
geo_characteristics	1.36	0.12	5.00
geo_info	0.09	0.00	0.10
getRPKM	1.43	0.13	1.54
reproduce_ranges	126.64	7.75	139.05
scale_counts	0.25	0.00	0.25
snaptron_query	1.37	0.00	7.19

name	user	system	elapsed
abstract_search	0.19	0.00	0.18
add_predictions	1.59	0.06	2.10
all_metadata	0.63	0.02	1.20
browse_study	0.2	0.0	0.2
coverage_matrix	0	0	0
download_study	1.83	0.06	2.55
expressed_regions	0	0	0
find_geo	0.62	0.01	1.67
geo_characteristics	1.67	0.05	5.11
geo_info	0.11	0.00	0.11
getRPKM	1.50	0.13	1.63
reproduce_ranges	142.80	5.59	152.95
scale_counts	0.21	0.08	0.30
snaptron_query	2.05	0.06	7.80