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CHECK report for GEOquery on tokay2

This page was generated on 2019-10-16 12:20:20 -0400 (Wed, 16 Oct 2019).

Package 669/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GEOquery 2.52.0
Sean Davis
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GEOquery
Branch: RELEASE_3_9
Last Commit: 3059331
Last Changed Date: 2019-05-02 11:53:05 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: GEOquery
Version: 2.52.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GEOquery.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GEOquery_2.52.0.tar.gz
StartedAt: 2019-10-16 04:02:07 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:08:35 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 388.3 seconds
RetCode: 0
Status:  OK  
CheckDir: GEOquery.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GEOquery.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GEOquery_2.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GEOquery.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GEOquery/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GEOquery' version '2.52.0'
* 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 'GEOquery' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 13.1Mb
  sub-directories of 1Mb or more:
    extdata  12.8Mb
* 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 ... NOTE
Warning: no function found corresponding to methods exports from 'GEOquery' for: 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** 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 ... NOTE
Warning: no function found corresponding to methods exports from 'GEOquery' for: 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'httr'
  All declared Imports should be used.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'GEOquery/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("Setting options('download.file.method.GEOquery'='auto')")
    packageStartupMessage("Setting options('GEOquery.inmemory.gpl'=FALSE)")

See section 'Good practice' in '?.onAttach'.

.parseGPLTxt: no visible global function definition for 'new'
.parseGPLWithLimits: no visible global function definition for 'new'
.parseGSMTxt: no visible global function definition for 'new'
.parseGSMWithLimits: no visible global function definition for 'new'
GDS2MA: no visible global function definition for 'new'
GDS2MA: no visible binding for global variable 'MA'
GDS2eSet: no visible global function definition for 'new'
fastTabRead: no visible global function definition for 'read.table'
fastTabRead: no visible global function definition for 'read.delim'
parseGDS: no visible global function definition for 'new'
parseGSE: no visible global function definition for 'new'
parseGSEMatrix: no visible global function definition for 'read.table'
parseGSEMatrix: no visible global function definition for 'new'
parseGSEMatrix: no visible binding for global variable '.'
parseGSEMatrix: no visible binding for global variable
  'characteristics'
parseGSEMatrix: no visible binding for global variable 'kvpair'
parseGSEMatrix: no visible binding for global variable 'accession'
parseGSEMatrix: no visible binding for global variable 'k'
parseGSEMatrix: no visible binding for global variable 'v'
parseGSEMatrix: no visible global function definition for 'as'
Undefined global functions or variables:
  . MA accession as characteristics k kvpair new read.delim read.table
  v
Consider adding
  importFrom("methods", "as", "new")
  importFrom("utils", "read.delim", "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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
getGEO 3.92    0.4    6.87
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
getGEO 3.84   0.29    6.72
* 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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/GEOquery.Rcheck/00check.log'
for details.

Installation output

GEOquery.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GEOquery_2.52.0.tar.gz && rm -rf GEOquery.buildbin-libdir && mkdir GEOquery.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GEOquery.buildbin-libdir GEOquery_2.52.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GEOquery_2.52.0.zip && rm GEOquery_2.52.0.tar.gz GEOquery_2.52.0.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 12.8M  100 12.8M    0     0  75.9M      0 --:--:-- --:--:-- --:--:-- 79.2M

install for i386

* installing *source* package 'GEOquery' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GEOquery'
    finding HTML links ... done
    GDS-class                               html  
    GEOData-accessors                       html  
    GEOData-class                           html  
    GEODataTable-class                      html  
    GPL-class                               html  
    GSE-class                               html  
    GSM-class                               html  
    coercion                                html  
    getDirListing                           html  
    getGEO                                  html  
    getGEOSuppFiles                         html  
    getGEOfile                              html  
    getGSEDataTables                        html  
    gunzip                                  html  
    parseGEO                                html  
    parseGSEMatrix                          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 'GEOquery' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GEOquery' as GEOquery_2.52.0.zip
* DONE (GEOquery)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GEOquery' successfully unpacked and MD5 sums checked

Tests output

GEOquery.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(GEOquery)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> 
> test_check("GEOquery")
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11413/matrix/GSE11413_series_matrix.txt.gz'
Content type 'application/x-gzip' length 3997 bytes
==================================================
downloaded 3997 bytes

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35683/matrix/GSE35683_series_matrix.txt.gz'
Content type 'application/x-gzip' length 5733793 bytes (5.5 MB)
==================================================
downloaded 5.5 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11595/matrix/GSE11595-GPL3906_series_matrix.txt.gz'
Content type 'application/x-gzip' length 59663 bytes (58 KB)
==================================================
downloaded 58 KB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11595/matrix/GSE11595-GPL4348_series_matrix.txt.gz'
Content type 'application/x-gzip' length 1528930 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34145/matrix/GSE34145-GPL15796_series_matrix.txt.gz'
Content type 'application/x-gzip' length 6643 bytes
==================================================
downloaded 6643 bytes

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34145/matrix/GSE34145-GPL6102_series_matrix.txt.gz'
Content type 'application/x-gzip' length 1428433 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71989/matrix/GSE71989_series_matrix.txt.gz'
Content type 'application/x-gzip' length 4240474 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53986/matrix/GSE53986_series_matrix.txt.gz'
Content type 'application/x-gzip' length 2848655 bytes (2.7 MB)
==================================================
downloaded 2.7 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99709/matrix/GSE99709_series_matrix.txt.gz'
Content type 'application/x-gzip' length 3386 bytes
==================================================
downloaded 3386 bytes

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27712/matrix/GSE27712-GPL4055_series_matrix.txt.gz'
Content type 'application/x-gzip' length 3312639 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27712/matrix/GSE27712-GPL6099_series_matrix.txt.gz'
Content type 'application/x-gzip' length 836112 bytes (816 KB)
==================================================
downloaded 816 KB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE2nnn/GSE2553/matrix/GSE2553_series_matrix.txt.gz'
Content type 'application/x-gzip' length 8480960 bytes (8.1 MB)
==================================================
downloaded 8.1 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1000/suppl//GSE1000_RAW.tar?tool=geoquery'
Content type 'application/x-tar' length 35307520 bytes (33.7 MB)
==================================================
downloaded 33.7 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM15nnn/GSM15789/suppl//GSM15789.cel.gz?tool=geoquery'
Content type 'application/x-gzip' length 3507725 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM15nnn/GSM15789/suppl//GSM15789.cel.gz?tool=geoquery'
Content type 'application/x-gzip' length 3507725 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

== testthat results  ===========================================================
[ OK: 203 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  83.75    6.12  159.39

GEOquery.Rcheck/tests_x64/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-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(GEOquery)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> 
> test_check("GEOquery")
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11413/matrix/GSE11413_series_matrix.txt.gz'
Content type 'application/x-gzip' length 3997 bytes
==================================================
downloaded 3997 bytes

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35683/matrix/GSE35683_series_matrix.txt.gz'
Content type 'application/x-gzip' length 5733793 bytes (5.5 MB)
==================================================
downloaded 5.5 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11595/matrix/GSE11595-GPL3906_series_matrix.txt.gz'
Content type 'application/x-gzip' length 59663 bytes (58 KB)
==================================================
downloaded 58 KB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11595/matrix/GSE11595-GPL4348_series_matrix.txt.gz'
Content type 'application/x-gzip' length 1528930 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34145/matrix/GSE34145-GPL15796_series_matrix.txt.gz'
Content type 'application/x-gzip' length 6643 bytes
==================================================
downloaded 6643 bytes

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34145/matrix/GSE34145-GPL6102_series_matrix.txt.gz'
Content type 'application/x-gzip' length 1428433 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71989/matrix/GSE71989_series_matrix.txt.gz'
Content type 'application/x-gzip' length 4240474 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53986/matrix/GSE53986_series_matrix.txt.gz'
Content type 'application/x-gzip' length 2848655 bytes (2.7 MB)
==================================================
downloaded 2.7 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99709/matrix/GSE99709_series_matrix.txt.gz'
Content type 'application/x-gzip' length 3386 bytes
==================================================
downloaded 3386 bytes

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27712/matrix/GSE27712-GPL4055_series_matrix.txt.gz'
Content type 'application/x-gzip' length 3312639 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27712/matrix/GSE27712-GPL6099_series_matrix.txt.gz'
Content type 'application/x-gzip' length 836112 bytes (816 KB)
==================================================
downloaded 816 KB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE2nnn/GSE2553/matrix/GSE2553_series_matrix.txt.gz'
Content type 'application/x-gzip' length 8480960 bytes (8.1 MB)
==================================================
downloaded 8.1 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1000/suppl//GSE1000_RAW.tar?tool=geoquery'
Content type 'application/x-tar' length 35307520 bytes (33.7 MB)
==================================================
downloaded 33.7 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM15nnn/GSM15789/suppl//GSM15789.cel.gz?tool=geoquery'
Content type 'application/x-gzip' length 3507725 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM15nnn/GSM15789/suppl//GSM15789.cel.gz?tool=geoquery'
Content type 'application/x-gzip' length 3507725 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

== testthat results  ===========================================================
[ OK: 203 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  78.68    4.53  140.28

Example timings

GEOquery.Rcheck/examples_i386/GEOquery-Ex.timings

nameusersystemelapsed
coercion000
getGEO3.920.406.87
getGEOSuppFiles0.020.020.11
getGEOfile000
getGSEDataTables0.360.030.76
gunzip000

GEOquery.Rcheck/examples_x64/GEOquery-Ex.timings

nameusersystemelapsed
coercion000
getGEO3.840.296.72
getGEOSuppFiles0.000.000.09
getGEOfile0.000.010.01
getGSEDataTables0.200.070.52
gunzip000