Question: Problem in the beginning
0
gravatar for zillurbmb51
4.6 years ago by
Puerto Rico
zillurbmb510 wrote:

Hi,

I am new in Bioconductor. I am learning and trying to install workflows. But 

> source("http://bioconductor.org/biocLite.R")
trying URL 'http://www.bioconductor.org/packages/3.0/bioc/bin/macosx/mavericks/contrib/3.1/BiocInstaller_1.16.1.tgz'
Content type 'application/x-gzip' length 49535 bytes (48 Kb)
opened URL
==================================================
downloaded 48 Kb

tar: Failed to set default locale

The downloaded binary packages are in
    /var/folders/7p/p1ktjtbs06l66qrvp04phbbh0000gn/T//RtmpxjypyM/downloaded_packages
Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help
>     biocLite("DESeq")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.1.
Installing package(s) 'DESeq'
also installing the dependencies 'IRanges', 'GenomeInfoDb', 'DBI', 'RSQLite', 'S4Vectors', 'XML', 'xtable', 'AnnotationDbi', 'annotate', 'BiocGenerics', 'Biobase', 'locfit', 'genefilter', 'geneplotter', 'RColorBrewer'

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/mavericks/contrib/3.1/DESeq_1.18.0.tgz'

Content type 'application/x-gzip' length 2137907 bytes (2.0 Mb)
opened URL
==================================================
downloaded 2.0 Mb

tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale

The downloaded binary packages are in
    /var/folders/7p/p1ktjtbs06l66qrvp04phbbh0000gn/T//RtmpxjypyM/downloaded_packages
Old packages: 'KernSmooth', 'MASS', 'Matrix', 'boot', 'class', 'cluster',
  'clusterGeneration', 'codetools', 'foreign', 'lattice', 'mgcv', 'nlme',
  'nnet', 'phangorn', 'rpart', 'spatial', 'survival'
Update all/some/none? [a/s/n]: 
a
also installing the dependency 'nnls'

downloaded 4.4 Mb

tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale
tar: Failed to set default locale

The downloaded binary packages are in
    /var/folders/7p/p1ktjtbs06l66qrvp04phbbh0000gn/T//RtmpxjypyM/downloaded_packages
> library(BiocInstaller)
> biocLite("DESeq")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.1.
Installing package(s) 'DESeq'
trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/mavericks/contrib/3.1/DESeq_1.18.0.tgz'
Content type 'application/x-gzip' length 2137907 bytes (2.0 Mb)
opened URL
==================================================
downloaded 2.0 Mb

tar: Failed to set default locale

The downloaded binary packages are in
    /var/folders/7p/p1ktjtbs06l66qrvp04phbbh0000gn/T//RtmpxjypyM/downloaded_packages
> vignette(“qrqc”)
Error: unexpected input in "vignette(‚"
> library(org.Hs.eg.db, quietly = TRUE)
Error in library(org.Hs.eg.db, quietly = TRUE) : 
  there is no package called 'org.Hs.eg.db'
> install.packages("org.Hs.eg.db")
--- Please select a CRAN mirror for use in this session ---
Warning message:
package 'org.Hs.eg.db' is not available (for R version 3.1.1) 
> library(org.Hs.eg.db, quietly = TRUE)
Error in library(org.Hs.eg.db, quietly = TRUE) : 
  there is no package called 'org.Hs.eg.db'
> > showMethods("cols")
Error: unexpected '>' in ">"
> showMethods("cols

> showMethods("cols")

Function "cols":
 <not an S4 generic function>
> biocLite(c("GenomicFeatures", "AnnotationDbi"))
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.1.
Installing package(s) 'GenomicFeatures' 'AnnotationDbi'
also installing the dependencies 'base64enc', 'iterators', 'brew', 'checkmate', 'digest', 'fail', 'sendmailR', 'stringr', 'foreach', 'BatchJobs', 'BBmisc', 'BiocParallel', 'XVector', 'zlibbioc', 'Rsamtools', 'GenomicAlignments', 'bitops', 'GenomicRanges', 'Biostrings', 'rtracklayer', 'biomaRt', 'RCurl'

trying URL 'http://cran.cs.wwu.edu/bin/macosx/mavericks/contrib/3.1/base64enc_0.1-2.tgz'
Content type 'application/x-gzip' length 22654 bytes (22 Kb)
opened URL
==================================================
downloaded 22 Kb

downloaded 27 Kb

trying URL 'http://cran.cs.wwu.edu/bin/macosx/mavericks/contrib/3.1/stringr_0.6.2.tgz'
Content type 'application/x-gzip' length 72797 bytes (71 Kb)
opened URL
==================================================
downloaded 71 Kb

trying URL 'http://cran.cs.wwu.edu/bin/macosx/mavericks/contrib/3.1/foreach_1.4.2.tgz'
Content type 'application/x-gzip' length 382280 bytes (373 Kb)
opened URL
==================================================
downloaded 373 Kb

trying URL 'http://cran.cs.wwu.edu/bin/macosx/mavericks/contrib/3.1/BatchJobs_1.5.tgz'
Content type 'application/x-gzip' length 409105 bytes (399 Kb)
opened URL
==================================================
downloaded 399 Kb

trying URL 'http://cran.cs.wwu.edu/bin/macosx/mavericks/contrib/3.1/BBmisc_1.9.tgz'
Content type 'application/x-gzip' length 274541 bytes (268 Kb)
opened URL
==================================================
downloaded 268 Kb

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/mavericks/contrib/3.1/BiocParallel_1.0.3.tgz'
Content type 'application/x-gzip' length 403291 bytes (393 Kb)
opened URL
==================================================
downloaded 393 Kb

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/mavericks/contrib/3.1/XVector_0.6.0.tgz'
Content type 'application/x-gzip' length 343748 bytes (335 Kb)
opened URL
==================================================
downloaded 335 Kb

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/mavericks/contrib/3.1/zlibbioc_1.12.0.tgz'
Content type 'application/x-gzip' length 124159 bytes (121 Kb)
opened URL
==================================================
downloaded 121 Kb

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/mavericks/contrib/3.1/Rsamtools_1.18.3.tgz'
Content type 'application/x-gzip' length 3856360 bytes (3.7 Mb)
opened URL
==================================================
downloaded 3.7 Mb

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/mavericks/contrib/3.1/GenomicAlignments_1.2.2.tgz'
Content type 'application/x-gzip' length 1308842 bytes (1.2 Mb)
opened URL
==================================================
downloaded 1.2 Mb

trying URL 'http://cran.cs.wwu.edu/bin/macosx/mavericks/contrib/3.1/bitops_1.0-6.tgz'
Content type 'application/x-gzip' length 23362 bytes (22 Kb)
opened URL
==================================================
downloaded 22 Kb

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/mavericks/contrib/3.1/GenomicRanges_1.18.4.tgz'
Content type 'application/x-gzip' length 1230796 bytes (1.2 Mb)
opened URL
==================================================
downloaded 1.2 Mb

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/mavericks/contrib/3.1/Biostrings_2.34.1.tgz'
Content type 'application/x-gzip' length 13544068 bytes (12.9 Mb)
opened URL
========
downloaded 2.1 Mb

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/mavericks/contrib/3.1/rtracklayer_1.26.2.tgz'
Content type 'application/x-gzip' length 1894179 bytes (1.8 Mb)
opened URL
======================================
downloaded 1.4 Mb

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/mavericks/contrib/3.1/biomaRt_2.22.0.tgz'
Content type 'application/x-gzip' length 406339 bytes (396 Kb)
opened URL
==================================================
downloaded 396 Kb

trying URL 'http://cran.cs.wwu.edu/bin/macosx/mavericks/contrib/3.1/RCurl_1.95-4.5.tgz'
Content type 'application/x-gzip' length 718964 bytes (702 Kb)
opened URL
==================================================
downloaded 702 Kb

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/mavericks/contrib/3.1/GenomicFeatures_1.18.3.tgz'
Content type 'application/x-gzip' length 1065297 bytes (1.0 Mb)
opened URL
==================================================
downloaded 1.0 Mb

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/mavericks/contrib/3.1/AnnotationDbi_1.28.1.tgz'
Content type 'application/x-gzip' length 4640495 bytes (4.4 Mb)
opened URL
==================================================
downloaded 4.4 Mb

tar: Failed to set default locale
tar: Failed to set default locale
tar: Error opening archive: (Empty error message)
Error: file '/var/folders/7p/p1ktjtbs06l66qrvp04phbbh0000gn/T//RtmpxjypyM/downloaded_packages/iterators_1.0.7.tgz' is not an OS X binary package
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 23256 != reported length 309616
2: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 15048 != reported length 40403
3: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 2192992 != reported length 13544068
4: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 1460685 != reported length 1894179
5: 'tar' returned non-zero exit code 1 
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.1.
> library(BiocInstaller)
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.1.
> BiocInstaller::useDevel()
Error: 'devel' version requires a more recent R
> biocValid()
[1] TRUE
> source("http://bioconductor.org/workflows.R")
Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help
> workflowInstall("arrays")
Warning: unable to access index for repository http://bioconductor.org/packages/3.0/workflows/bin/macosx/mavericks/contrib/3.1

   package 'arrays' is available as a source package but not as a binary

Warning message:
package 'arrays' is not available (for R version 3.1.1) 
> library(affy)
Error in library(affy) : there is no package called 'affy'
> library(limma)
Error in library(limma) : there is no package called 'limma'
> workflowInstall("arrays")
Warning: unable to access index for repository http://bioconductor.org/packages/3.0/workflows/bin/macosx/mavericks/contrib/3.1

   package 'arrays' is available as a source package but not as a binary

Warning message:
package 'arrays' is not available (for R version 3.1.1) 
> library(affy)

affy • 1.9k views
ADD COMMENTlink written 4.6 years ago by zillurbmb510

You will have to get tar to succeed.

There is a potentially relevant suggestion at

http://davidprakash.blogspot.com/2011/05/r-error-tar-failed-to-set-default.html

If that does not work please read the posting guide and provide more details about your environment

 

ADD REPLYlink written 4.6 years ago by Vincent J. Carey, Jr.6.3k
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