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BioC 3.5: BUILD report for DupChecker on veracruz2

This page was generated on 2017-08-16 13:32:02 -0400 (Wed, 16 Aug 2017).

Package 373/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DupChecker 1.14.0
"Quanhu SHENG"
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/DupChecker
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  ERROR  skipped  skipped 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded [ ERROR ] skipped  skipped 

Summary

Package: DupChecker
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data DupChecker
StartedAt: 2017-08-15 20:48:45 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 20:49:24 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 39.1 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data DupChecker
###
##############################################################################
##############################################################################


* checking for file ‘DupChecker/DESCRIPTION’ ... OK
* preparing ‘DupChecker’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Downloading data to  /tmp/DupChecker ...
Dataset GSE1478 is downloading to /tmp/DupChecker/GSE1478 ...
Downloading file ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE1478/filelist.txt ...
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE1478/filelist.txt'
Content type 'unknown' length 392 bytes
==================================================
Downloading file ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE1478/GSE1478_RAW.tar ...
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE1478/GSE1478_RAW.tar'
Content type 'unknown' length 4423680 bytes (4.2 MB)
==================================================
Untar file /tmp/DupChecker/GSE1478/GSE1478_RAW.tar ...
Decompressing file /tmp/DupChecker/GSE1478/GSM25148.CEL.gz ...
Decompressing file /tmp/DupChecker/GSE1478/GSM25148.EXP.gz ...
Decompressing file /tmp/DupChecker/GSE1478/GSM25148.RPT.gz ...
Decompressing file /tmp/DupChecker/GSE1478/GSM25149.CEL.gz ...
Decompressing file /tmp/DupChecker/GSE1478/GSM25149.EXP.gz ...
Decompressing file /tmp/DupChecker/GSE1478/GSM25149.RPT.gz ...
Dataset GSE1478 has been downloaded.
Dataset E-MEXP-3872 is downloading to /tmp/DupChecker/E-MEXP-3872 ...
Downloading file ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-3872/E-MEXP-3872.idf.txt ...
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-3872/E-MEXP-3872.idf.txt'
Content type 'unknown' length 4044 bytes
==================================================
Downloading file ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-3872/E-MEXP-3872.processed.1.zip ...
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-3872/E-MEXP-3872.processed.1.zip'
Content type 'unknown' length 607386 bytes (593 KB)
==================================================
Decompressing file /tmp/DupChecker/E-MEXP-3872/E-MEXP-3872.processed.1.zip ...
Downloading file ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-3872/E-MEXP-3872.raw.1.zip ...
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-3872/E-MEXP-3872.raw.1.zip'
Content type 'unknown' length 5074340 bytes (4.8 MB)
==================================================
Decompressing file /tmp/DupChecker/E-MEXP-3872/E-MEXP-3872.raw.1.zip ...
Downloading file ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-3872/E-MEXP-3872.sdrf.txt ...
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-3872/E-MEXP-3872.sdrf.txt'
Content type 'unknown' length 1113 bytes
==================================================
Dataset E-MEXP-3872 has been downloaded.
calculate and validate files, make sure the directory is readable.
Calculating md5 for /tmp/DupChecker/E-MEXP-3872/JM101124PTN049-2_01.CEL...
Calculating md5 for /tmp/DupChecker/GSE1478/GSM25148.CEL...
Calculating md5 for /tmp/DupChecker/GSE1478/GSM25149.CEL...
Dataset GSE1478 is downloading to /tmp/DupChecker/GSE1478 ...
Quitting from lines 113-118 (DupChecker.Rnw) 
Error: processing vignette 'DupChecker.Rnw' failed with diagnostics:
Server denied you to change to the given directory
Execution halted