Unable to install Bioconductor packages with biocLite...

gmpune · 12-09-2013, 02:27 AM

Hi,

I'm very new to R/Bioconductor. Presently I'm trying to fetch and install BioC packages using the biocLite route, but it's stumbling. Here's the error I get:

> source("http://bioconductor.org/biocLite.R")
Error in source("http://bioconductor.org/biocLite.R") :
http://bioconductor.org/biocLite.R:1:1: unexpected '<'
1: <
^

Could somebody please suggest a way out? I'm on Windows 7 and behind a proxy server (no username/pwd authentication required though).

Thanks a lot and good day!

dpryan · 12-09-2013, 02:41 AM

I wonder if your proxy is screwing things up. You can download that file, double check that it's not corrupted, and then try sourcing it directly. What version of R are you using (just post the output of sessionInfo() ).

gmpune · 12-09-2013, 02:47 AM

Thanks for replying, dpryan. But I'm not sure I understand you correctly. Which file are you referring to? btw I'm on R v3.0.1:

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252
[3] LC_MONETARY=English_India.1252 LC_NUMERIC=C
[5] LC_TIME=English_India.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

Thanks again.

dpryan · 12-09-2013, 03:37 AM

The file I'm referring to is biocLite.R. You can just download it directly and double check it, since that's what's producing the error.

gmpune · 12-09-2013, 08:48 PM

I downloaded the biocLite.R file to a local folder and then tried running it directly. Seems like an html problem:

> biocLite("NOISeq")
Line starting '<HTML><HEAD> ...' is malformed!, using
'http://bioconductor.org/packages/2.12/bioc'
Error: Line starting '<HTML><HEAD> ...' is malformed!

Is there something obvious I'm missing?
Thanks.

rxzlmn · 12-09-2013, 10:24 PM

whatever is being downloaded contains HTML tags, so it is not the correct file. do not use a browser and 'save page', rather download it directly, or open the document in the browser and copy out the text.

gmpune · 12-10-2013, 01:14 AM

Hi rxzlmn,

Actually that's what I did (so hard to understand the html tags...), I just opened the biocLite.R file in Firefox and then copy-pasted it into Notepad++.

amitbik · 01-25-2014, 02:10 AM

Hi There..

I have installed R version 3.0.2 when i am trying to update bioconducter packages i am geting following error

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
Warning message:
installed directory not writable, cannot update packages 'foreign', 'spatial',
'survival'

I have change the installed directory permission also but still i am geting this error.
can anyone help to find out the error..

Thanks..

rboettcher · 01-26-2014, 11:03 PM

You can try to run R via sudo and see if the problems persist.

amitbik · 01-27-2014, 02:23 AM

Thanks... rboettcher

It worked for me..

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12-09-2013, 02:27 AM	#1
gmpune Junior Member Location: India Join Date: Dec 2013 Posts: 4	Unable to install Bioconductor packages with biocLite... Hi, I'm very new to R/Bioconductor. Presently I'm trying to fetch and install BioC packages using the biocLite route, but it's stumbling. Here's the error I get: > source("http://bioconductor.org/biocLite.R") Error in source("http://bioconductor.org/biocLite.R") : http://bioconductor.org/biocLite.R:1:1: unexpected '<' 1: < ^ Could somebody please suggest a way out? I'm on Windows 7 and behind a proxy server (no username/pwd authentication required though). Thanks a lot and good day!

01-25-2014, 02:10 AM	#8
amitbik Member Location: Italy Join Date: May 2013 Posts: 50	Error in updating biocLite() package Hi There.. I have installed R version 3.0.2 when i am trying to update bioconducter packages i am geting following error > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help > biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. Warning message: installed directory not writable, cannot update packages 'foreign', 'spatial', 'survival' I have change the installed directory permission also but still i am geting this error. can anyone help to find out the error.. Thanks..

12-09-2013, 02:41 AM	#2
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	I wonder if your proxy is screwing things up. You can download that file, double check that it's not corrupted, and then try sourcing it directly. What version of R are you using (just post the output of sessionInfo() ).

12-09-2013, 02:47 AM	#3
gmpune Junior Member Location: India Join Date: Dec 2013 Posts: 4	Thanks for replying, dpryan. But I'm not sure I understand you correctly. Which file are you referring to? btw I'm on R v3.0.1: > sessionInfo() R version 3.0.1 (2013-05-16) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252 [3] LC_MONETARY=English_India.1252 LC_NUMERIC=C [5] LC_TIME=English_India.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base Thanks again.

12-09-2013, 03:37 AM	#4
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	The file I'm referring to is biocLite.R. You can just download it directly and double check it, since that's what's producing the error.

12-09-2013, 08:48 PM	#5
gmpune Junior Member Location: India Join Date: Dec 2013 Posts: 4	I downloaded the biocLite.R file to a local folder and then tried running it directly. Seems like an html problem: > biocLite("NOISeq") Line starting '<HTML><HEAD> ...' is malformed!, using 'http://bioconductor.org/packages/2.12/bioc' Error: Line starting '<HTML><HEAD> ...' is malformed! Is there something obvious I'm missing? Thanks.

12-09-2013, 10:24 PM	#6
rxzlmn Junior Member Location: Singapore Join Date: Nov 2013 Posts: 8	whatever is being downloaded contains HTML tags, so it is not the correct file. do not use a browser and 'save page', rather download it directly, or open the document in the browser and copy out the text.

12-10-2013, 01:14 AM	#7
gmpune Junior Member Location: India Join Date: Dec 2013 Posts: 4	Hi rxzlmn, Actually that's what I did (so hard to understand the html tags...), I just opened the biocLite.R file in Firefox and then copy-pasted it into Notepad++.

01-26-2014, 11:03 PM	#9
rboettcher Member Location: Berlin Join Date: Oct 2010 Posts: 71	You can try to run R via sudo and see if the problems persist.

01-27-2014, 02:23 AM	#10
amitbik Member Location: Italy Join Date: May 2013 Posts: 50	Thanks... rboettcher It worked for me..