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BioC 3.2: CHECK report for DAVIDQuery on zin1

This page was generated on 2016-04-23 10:11:07 -0700 (Sat, 23 Apr 2016).

Package 251/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAVIDQuery 1.30.0
Roger Day
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/DAVIDQuery
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ ERROR ]
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  ERROR  skipped  skipped 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  ERROR  OK 

Summary

Package: DAVIDQuery
Version: 1.30.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings DAVIDQuery_1.30.0.tar.gz
StartedAt: 2016-04-22 23:52:52 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:53:23 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 31.4 seconds
RetCode: 1
Status:  ERROR 
CheckDir: DAVIDQuery.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings DAVIDQuery_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/DAVIDQuery.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DAVIDQuery/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAVIDQuery’ version ‘1.30.0’
* 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 ‘DAVIDQuery’ can be installed ... [1s/1s] WARNING
Found the following significant warnings:
  Warning: Package 'DAVIDQuery' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.2-bioc/meat/DAVIDQuery.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘RCurl’
  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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘DAVIDQuery/R/zzz.R’:
  .onAttach calls:
    cat("This is DAVIDQuery Version ", DQVersion, " ", DQdate, "\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.

read.delim0: no visible global function definition for ‘CFILE’
read.delim0: no visible global function definition for ‘curlPerform’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘read.delim0’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘DAVIDQuery-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: testGene2Gene
> ### Title: Test DAVID gene2gene tool
> ### Aliases: testGene2Gene
> ### Keywords: database
> 
> ### ** Examples
> 
> 	testGene2Gene(details=FALSE)  
$`Gene Group 1`
$`Gene Group 1`$type
[1] "Enrichment Score"

$`Gene Group 1`$value
[1] 3.366741

$`Gene Group 1`$details
  AFFYMETRIX_3PRIME_IVT_ID
3                 33530_AT
4                 32469_AT
5                 31987_AT
6                 37968_AT
7                1112_G_AT
8                 33077_AT
9               35956_S_AT
                                                                                                                     Gene Name
3                                                                    carcinoembryonic antigen-related cell adhesion molecule 8
4                                                                    carcinoembryonic antigen-related cell adhesion molecule 3
5                                                                                                kin of IRRE like (Drosophila)
6                                                                                   natural cytotoxicity triggering receptor 3
7                                                                                              neural cell adhesion molecule 1
8                                                 sidekick homolog 1, cell adhesion molecule (chicken); hypothetical LOC730351
9 pregnancy specific beta-1-glycoprotein 7; pregnancy specific beta-1-glycoprotein 8; pregnancy specific beta-1-glycoprotein 4


$`Gene Group 2`
$`Gene Group 2`$type
[1] "Enrichment Score"

$`Gene Group 2`$value
[1] 1.977116

$`Gene Group 2`$details
   AFFYMETRIX_3PRIME_IVT_ID
12                  1575_AT
13                 33685_AT
14                 40294_AT
15               39469_S_AT
16                 32439_AT
                                                                Gene Name
12                 ATP-binding cassette, sub-family B (MDR/TAP), member 1
13                                     ATPase, class I, type 8B, member 3
14                 ATP-binding cassette, sub-family B (MDR/TAP), member 9
15 ATPase, aminophospholipid transporter-like, class I, type 8A, member 2
16                             ATPase, H+/K+ exchanging, beta polypeptide


$`Gene Group 3`
$`Gene Group 3`$type
[1] "Enrichment Score"

$`Gene Group 3`$value
[1] 1.809295

$`Gene Group 3`$details
   AFFYMETRIX_3PRIME_IVT_ID
19               37953_S_AT
20                 34436_AT
21                 40317_AT
22                 37097_AT
                                               Gene Name
19        amiloride-sensitive cation channel 2, neuronal
20 solute carrier family 17 (sodium phosphate), member 3
21        amiloride-sensitive cation channel 1, neuronal
22 solute carrier family 17 (sodium phosphate), member 1


$`Gene Group 4`
$`Gene Group 4`$type
[1] "Enrichment Score"

$`Gene Group 4`$value
[1] 1.331826

$`Gene Group 4`$details
   AFFYMETRIX_3PRIME_IVT_ID                               Gene Name
25                 38945_AT metal-regulatory transcription factor 1
26                 41113_AT                 zinc finger protein 500
27               34606_S_AT       activating transcription factor 7
28                 33922_AT PR domain containing 2, with ZNF domain


attr(,"ids")
[1] "33246_AT,32469_AT,1786_AT,32680_AT,1355_G_AT,37968_AT,33530_AT,31987_AT,35956_S_AT,35956_S_AT,1112_G_AT,33077_AT,1331_S_AT,40350_AT,37968_AT,38926_AT,37953_S_AT,34436_AT,37097_AT,32439_AT,35121_AT,40317_AT,39469_S_AT,32439_AT,33685_AT,40294_AT,1575_AT,39187_AT,34720_AT,41489_AT,35439_AT,39698_AT,40790_AT,33922_AT,39908_AT,41113_AT,34606_S_AT,37711_AT,38945_AT,32073_AT"
attr(,"tool")
[1] "gene2gene"
attr(,"type")
[1] "AFFYMETRIX_3PRIME_IVT_ID"
> 		### Run example from http://david.abcc.ncifcrf.gov/gene2gene.jsp
> 	testGene2Gene(ids=idExampleList, type="ENTREZ_GENE_ID", details=FALSE)
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  Warning: downloadFileName is not found in reply html. 

Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  incomplete final line found by readTableHeader on '/tmp/Rtmp6m87To/file2e22bfd96'
Error in if (tool == "geneReportFull") { : argument is of length zero
Calls: testGene2Gene -> DAVIDQuery -> formatDAVIDResult
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, 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/DAVIDQuery.Rcheck/00check.log’
for details.

DAVIDQuery.Rcheck/00install.out:

* installing *source* package ‘DAVIDQuery’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
This is DAVIDQuery Version  1.30.0   2015-07-20 
Warning: Package 'DAVIDQuery' is deprecated and will be removed from
  Bioconductor version 3.3
* DONE (DAVIDQuery)

DAVIDQuery.Rcheck/DAVIDQuery-Ex.timings:

nameusersystemelapsed
DAVIDQuery0.0500.0076.899
bracketedStrings0.0010.0000.001
convertIDList0.0010.0000.000
findInBrackets0.0010.0000.000
getAffyChipTypes0.0000.0000.001
getAffyProbesetList0.2430.0042.375
getAnnotationChoices0.0010.0000.000
getIdConversionChoices0.0010.0000.001
requestIDConversion000