DAVIDQuery 1.31.0
Roger Day
| Snapshot Date: 2016-05-01 16:20:05 -0700 (Sun, 01 May 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DAVIDQuery | | Last Changed Rev: 109592 / Revision: 116959 | | Last Changed Date: 2015-10-13 12:59:53 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | | |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | ERROR | skipped | skipped | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DAVIDQuery_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/DAVIDQuery.Rcheck’
* using R version 3.3.0 RC (2016-04-28 r70561)
* 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 ‘1.31.0’
* 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-3.4-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'.
.onAttach: no visible global function definition for
‘packageDescription’
getAffyChipTypes: no visible global function definition for
‘assignInNamespace’
getAnnotationChoices: no visible global function definition for
‘assignInNamespace’
getIdConversionChoices: no visible global function definition for
‘assignInNamespace’
read.delim0: no visible global function definition for ‘CFILE’
read.delim0: no visible global function definition for ‘curlPerform’
Undefined global functions or variables:
CFILE assignInNamespace curlPerform packageDescription
Consider adding
importFrom("utils", "assignInNamespace", "packageDescription")
to your NAMESPACE file.
* 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/RtmpDjo3kv/filea9e2bcaceca'
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-3.4-bioc/meat/DAVIDQuery.Rcheck/00check.log’
for details.