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BioC 3.5: CHECK report for GEOquery on malbec2

This page was generated on 2017-10-18 14:12:42 -0400 (Wed, 18 Oct 2017).

Package 552/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GEOquery 2.42.0
Sean Davis
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/GEOquery
Branch: RELEASE_3_5
Last Commit: c26adef
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ ERROR ]
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: GEOquery
Version: 2.42.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GEOquery_2.42.0.tar.gz
StartedAt: 2017-10-17 23:36:17 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 23:38:19 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 122.3 seconds
RetCode: 1
Status:  ERROR 
CheckDir: GEOquery.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GEOquery_2.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GEOquery.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GEOquery/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GEOquery’ version ‘2.42.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GEOquery’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 13.9Mb
  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
* 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
'library' or 'require' call to ‘limma’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘Biobase’
  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'.

GDS2MA: no visible binding for global variable ‘MA’
fastTabRead: no visible global function definition for ‘read.table’
fastTabRead: no visible global function definition for ‘read.delim’
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’
getGEOfile: no visible global function definition for ‘download.file’
getGSEDataTables : <anonymous>: no visible global function definition
  for ‘read.delim’
parseGSEMatrix: no visible global function definition for ‘read.table’
parseGSEMatrix: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  MA download.file read.delim read.table
Consider adding
  importFrom("utils", "download.file", "read.delim", "read.table")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  FAILURE in testSuppFileSupport: Error in checkEquals(1, nrow(fres)) : Mean relative difference: 1
  
  
  Test files with failing tests
  
     test_ShortGSE.R 
       testShortGSE 
  
     test_SuppFileSupport.R 
       testSuppFileSupport 
  
  
  Error in BiocGenerics:::testPackage("GEOquery") : 
    unit tests failed for package GEOquery
  Execution halted
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/GEOquery.Rcheck/00check.log’
for details.

runTests.Rout.fail:


R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> BiocGenerics:::testPackage("GEOquery")

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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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)
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35683/matrix/
OK
Found 1 file(s)
GSE35683_series_matrix.txt.gz
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

File stored at: 
/tmp/RtmpgTrG37/GPL570.soft
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11413/matrix/
OK
Found 1 file(s)
GSE11413_series_matrix.txt.gz
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

File stored at: 
/tmp/RtmpgTrG37/GPL5082.soft
File stored at: 
/tmp/RtmpgTrG37/GPL97.annot.gz
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

File stored at: 
/tmp/RtmpgTrG37/GPL96.soft
File stored at: 
/tmp/RtmpgTrG37/GSM11805.soft
File stored at: 
/tmp/RtmpgTrG37/GPL4133.soft
File stored at: 
/tmp/RtmpgTrG37/GSE1563.soft.gz
Parsing....
Found 63 entities...
GPL8300 (1 of 63 entities)
GSM26805 (2 of 63 entities)
GSM26806 (3 of 63 entities)
GSM26807 (4 of 63 entities)
GSM26808 (5 of 63 entities)
GSM26809 (6 of 63 entities)
GSM26810 (7 of 63 entities)
GSM26811 (8 of 63 entities)
GSM26812 (9 of 63 entities)
GSM26813 (10 of 63 entities)
GSM26814 (11 of 63 entities)
GSM26815 (12 of 63 entities)
GSM26816 (13 of 63 entities)
GSM26817 (14 of 63 entities)
GSM26818 (15 of 63 entities)
GSM26819 (16 of 63 entities)
GSM26820 (17 of 63 entities)
GSM26821 (18 of 63 entities)
GSM26822 (19 of 63 entities)
GSM26823 (20 of 63 entities)
GSM26824 (21 of 63 entities)
GSM26825 (22 of 63 entities)
GSM26826 (23 of 63 entities)
GSM26827 (24 of 63 entities)
GSM26828 (25 of 63 entities)
GSM26829 (26 of 63 entities)
GSM26830 (27 of 63 entities)
GSM26831 (28 of 63 entities)
GSM26832 (29 of 63 entities)
GSM26833 (30 of 63 entities)
GSM26834 (31 of 63 entities)
GSM26835 (32 of 63 entities)
GSM26836 (33 of 63 entities)
GSM26837 (34 of 63 entities)
GSM26838 (35 of 63 entities)
GSM26839 (36 of 63 entities)
GSM26840 (37 of 63 entities)
GSM26841 (38 of 63 entities)
GSM26842 (39 of 63 entities)
GSM26843 (40 of 63 entities)
GSM26844 (41 of 63 entities)
GSM26845 (42 of 63 entities)
GSM26846 (43 of 63 entities)
GSM26847 (44 of 63 entities)
GSM26848 (45 of 63 entities)
GSM26849 (46 of 63 entities)
GSM26850 (47 of 63 entities)
GSM26851 (48 of 63 entities)
GSM26852 (49 of 63 entities)
GSM26853 (50 of 63 entities)
GSM26854 (51 of 63 entities)
GSM26855 (52 of 63 entities)
GSM26856 (53 of 63 entities)
GSM26857 (54 of 63 entities)
GSM26858 (55 of 63 entities)
GSM26859 (56 of 63 entities)
GSM26860 (57 of 63 entities)
GSM26861 (58 of 63 entities)
GSM26862 (59 of 63 entities)
GSM26863 (60 of 63 entities)
GSM26864 (61 of 63 entities)
GSM26865 (62 of 63 entities)
GSM26866 (63 of 63 entities)
File stored at: 
/tmp/RtmpgTrG37/GPL15505.soft
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34145/matrix/
OK
Found 3 file(s)
/geo/series/GSE34nnn/GSE34145/
Timing stopped at: 0.092 0.004 0.3
Error in file(con, "r") : cannot open the connection
In addition: There were 50 or more warnings (use warnings() to see the first 50)
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11595/matrix/
OK
Found 2 file(s)
GSE11595-GPL3906_series_matrix.txt.gz
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

File stored at: 
/tmp/RtmpgTrG37/GPL3906.soft
GSE11595-GPL4348_series_matrix.txt.gz
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

File stored at: 
/tmp/RtmpgTrG37/GPL4348.soft
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1000/suppl/
OK
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1000/suppl//GSE1000_RAW.tar'
Content type 'application/x-tar' length 35307520 bytes (33.7 MB)
==================================================
downloaded 33.7 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1000/suppl//filelist.txt'
Content type 'text/plain' length 621 bytes
==================================================
downloaded 621 bytes

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

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

Timing stopped at: 0.772 0.18 4.392
Error in checkEquals(1, nrow(fres)) : Mean relative difference: 1

In addition: Warning messages:
1: In read.table(file = file, header = header, sep = sep, quote = quote,  :
  not all columns named in 'colClasses' exist
2: In read.table(file = file, header = header, sep = sep, quote = quote,  :
  not all columns named in 'colClasses' exist
3: In download.file(file.path(url, i), destfile = file.path(storedir,  :
  URL https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM15nnn/GSM15789/suppl///geo/samples/GSM15nnn/GSM15789/: cannot open destfile '/tmp/RtmpgTrG37/GSM15789//geo/samples/GSM15nnn/GSM15789/', reason 'No such file or directory'
4: In download.file(file.path(url, i), destfile = file.path(storedir,  :
  download had nonzero exit status
File stored at: 
/tmp/RtmpgTrG37/GDS10.soft.gz
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE2nnn/GSE2553/matrix/
OK
Found 1 file(s)
GSE2553_series_matrix.txt.gz
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



RUNIT TEST PROTOCOL -- Tue Oct 17 23:38:16 2017 
*********************************************** 
Number of test functions: 14 
Number of errors: 1 
Number of failures: 1 

 
1 Test Suite : 
GEOquery RUnit Tests - 14 test functions, 1 error, 1 failure
ERROR in testShortGSE: Error in file(con, "r") : cannot open the connection
FAILURE in testSuppFileSupport: Error in checkEquals(1, nrow(fres)) : Mean relative difference: 1


Test files with failing tests

   test_ShortGSE.R 
     testShortGSE 

   test_SuppFileSupport.R 
     testSuppFileSupport 


Error in BiocGenerics:::testPackage("GEOquery") : 
  unit tests failed for package GEOquery
Execution halted

GEOquery.Rcheck/00install.out:

* installing *source* package ‘GEOquery’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GEOquery)

GEOquery.Rcheck/GEOquery-Ex.timings:

nameusersystemelapsed
GDS2MA000
getGEO000
getGEOSuppFiles000
getGEOfile0.0000.0000.001
getGSEDataTables0.2720.0200.704