Getting error in DESeq Installation

Yogesh Gupta

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Oct 24, 2016, 1:02:00 AM10/24/16

to trinityrnaseq-users

Dear all,

I am not able to install DESeq, can you suggest any solution?

ERROR:

> install.packages("DESeq")

Installing package into ‘/usr/lib64/R/library’

(as ‘lib’ is unspecified)

--- Please select a CRAN mirror for use in this session ---

HTTPS CRAN mirror

1: 0-Cloud [https] 2: Algeria [https]

3: Australia (Melbourne) [https] 4: Australia (Perth) [https]

5: Austria [https] 6: Belgium (Ghent) [https]

7: Brazil (RJ) [https] 8: Brazil (SP 1) [https]

9: Bulgaria [https] 10: Canada (MB) [https]

11: Chile [https] 12: China (Beijing) [https]

13: China (Hefei) [https] 14: Colombia (Cali) [https]

15: Czech Republic [https] 16: Denmark [https]

17: France (Lyon 1) [https] 18: France (Lyon 2) [https]

19: France (Marseille) [https] 20: France (Montpellier) [https]

21: France (Paris 2) [https] 22: Germany (Falkenstein) [https]

23: Germany (Münster) [https] 24: Iceland [https]

25: India [https] 26: Ireland [https]

27: Italy (Padua) [https] 28: Japan (Tokyo) [https]

29: Malaysia [https] 30: Mexico (Mexico City) [https]

31: New Zealand [https] 32: Norway [https]

33: Philippines [https] 34: Russia (Moscow) [https]

35: Serbia [https] 36: Spain (A Coruña) [https]

37: Spain (Madrid) [https] 38: Switzerland [https]

39: Taiwan (Chungli) [https] 40: Turkey (Denizli) [https]

41: UK (Bristol) [https] 42: UK (Cambridge) [https]

43: UK (London 1) [https] 44: USA (CA 1) [https]

45: USA (IA) [https] 46: USA (KS) [https]

47: USA (MI 1) [https] 48: USA (TN) [https]

49: USA (TX) [https] 50: USA (WA) [https]

51: (HTTP mirrors)

Selection: 25

Warning message:

package ‘DESeq’ is not available (for R version 3.3.1)

>

Thanks

Yogesh

--

Yogesh Gupta

Postdoctoral Researcher

Department of Biological Science

Seoul National University

Seoul, South Korea

web) http://biosci.snu.ac.kr/jiyounglee

Cell No. +82-10-6453-0716

Mark Chapman

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Oct 24, 2016, 2:09:21 AM10/24/16

to Yogesh Gupta, trinityrnaseq-users

the DESeq website says this, have you tried it?:

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq")

--Mark

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Dr. Mark A. Chapman

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SO17 1BJ

Yogesh Gupta

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Oct 24, 2016, 2:19:16 AM10/24/16

to Mark Chapman, trinityrnaseq-users

Dear Dr. Mark

When I type this. it shows below massage.

> source("https://bioconductor.org/biocLite.R")

Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help

when I type > biocLite("BiocUpgrade")

it shows this error:

Error: Bioconductor version 3.4 cannot be upgraded with R version 3.3.1

Thanks

Yogesh

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--
Dr. Mark A. Chapman
M.Ch...@soton.ac.uk
+44 (0)2380 594396
------------------------------------
Centre for Biological Sciences
University of Southampton
Life Sciences Building 85
Highfield Campus
Southampton
SO17 1BJ

Yogesh Gupta

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Oct 24, 2016, 2:22:32 AM10/24/16

to Mark Chapman, trinityrnaseq-users

Dear Dr. Mark

I tried several ways to install it, sometimes it shows this error:

package ‘DESeq’ is not available (for R version 3.3.1)

> source("http://www.Bioconductor.org/biocLite.R")

Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help

> biocLite("BiocUpgrade")

Error: Bioconductor version 3.4 cannot be upgraded with R version 3.3.1

Can you suggest me I How I can resolve it.

Thanks

Yogesh

Yogesh Gupta

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Oct 24, 2016, 2:25:30 AM10/24/16

to Mark Chapman, trinityrnaseq-users

Dear Dr. Mark

When I run cammand as you suggested it shows this error:

> source("https://bioconductor.org/biocLite.R")

Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help

> biocLite("DESeq")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.1 (2016-06-21).

Installing package(s) ‘DESeq’

also installing the dependencies ‘XML’, ‘RCurl’, ‘annotate’, ‘genefilter’, ‘geneplotter’

trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.4.tar.gz'

Content type 'unknown' length 1599214 bytes (1.5 MB)

==================================================

downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/src/contrib/RCurl_1.95-4.8.tar.gz'

Content type 'unknown' length 916934 bytes (895 KB)

==================================================

downloaded 895 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/annotate_1.52.0.tar.gz'

Content type 'unknown' length 1861023 bytes (1.8 MB)

==================================================

downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/genefilter_1.56.0.tar.gz'

Content type 'unknown' length 1407436 bytes (1.3 MB)

==================================================

downloaded 1.3 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/geneplotter_1.52.0.tar.gz'

Content type 'unknown' length 1426298 bytes (1.4 MB)

==================================================

downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/DESeq_1.26.0.tar.gz'

Content type 'unknown' length 1698987 bytes (1.6 MB)

==================================================

downloaded 1.6 MB

* installing *source* package ‘XML’ ...

** package ‘XML’ successfully unpacked and MD5 sums checked

checking for gcc... gcc

checking for C compiler default output file name... a.out

checking whether the C compiler works... yes

checking whether we are cross compiling... no

checking for suffix of executables...

checking for suffix of object files... o

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking how to run the C preprocessor... gcc -E

checking for sed... /usr/bin/sed

checking for pkg-config... /usr/bin/pkg-config

checking for xml2-config... no

Cannot find xml2-config

ERROR: configuration failed for package ‘XML’

* removing ‘/usr/lib64/R/library/XML’

* installing *source* package ‘RCurl’ ...

** package ‘RCurl’ successfully unpacked and MD5 sums checked

checking for curl-config... no

Cannot find curl-config

ERROR: configuration failed for package ‘RCurl’

* removing ‘/usr/lib64/R/library/RCurl’

ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘annotate’

* removing ‘/usr/lib64/R/library/annotate’

ERROR: dependency ‘annotate’ is not available for package ‘genefilter’

* removing ‘/usr/lib64/R/library/genefilter’

ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’

* removing ‘/usr/lib64/R/library/geneplotter’

ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq’

* removing ‘/usr/lib64/R/library/DESeq’

The downloaded source packages are in

‘/tmp/RtmpsMJs05/downloaded_packages’

Updating HTML index of packages in '.Library'

Making 'packages.html' ... done

Warning messages:

1: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘XML’ had non-zero exit status

2: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘RCurl’ had non-zero exit status

3: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘annotate’ had non-zero exit status

4: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘genefilter’ had non-zero exit status

5: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘geneplotter’ had non-zero exit status

6: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘DESeq’ had non-zero exit status

Thanks

'Yogesh

Mark Chapman

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Oct 24, 2016, 2:28:53 AM10/24/16

to Yogesh Gupta, trinityrnaseq-users

It looks like the R version you have isn't compatible then. I'd suggest asking the DESeq team about this as its not run by trinity folks, or could you use an older version of R?

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