search

lgatto / MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics
http://lgatto.github.io/MSnbase/
124 stars 50 forks source link

Not able to install MSnbase #62

Closed bbdamodaran closed 8 years ago

bbdamodaran commented 8 years ago

I tried to install MSnbase package in R (linux), but I couldn't do it. I did as follows

source("http://bioconductor.org/biocLite.R") biocLite()

Then biocLite("MSnbase")

I got following message at the end.

Warning messages: 1: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘mzR’ had non-zero exit status 2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘MSnbase’ had non-zero exit status

When I tried library(MSnbase)

The library MSnbase package was not found.

Please help me to install this package ( I searched in google, but I couldn't find the solution).

Thanks

sgibb commented 8 years ago

Could you please provide the complete output of:

source("http://bioconductor.org/biocLite.R")
biocLite("mzR")

and

sessionInfo()
bbdamodaran commented 8 years ago

Thanks for your message. Please see the following

biocLite("mzR") BioC_mirror: https://bioconductor.org Using Bioconductor 3.2 (BiocInstaller 1.19.14), R 3.2.2 (2015-08-14). Installing package(s) ‘mzR’ essai de l'URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/mzR_2.3.2.tar.gz'

Content type 'application/x-gzip' length 14656653 bytes (14.0 MB)

downloaded 14.0 MB

The downloaded source packages are in ‘/tmp/Rtmpoe9gSB/downloaded_packages’ Old packages: 'abind', 'caTools', 'clue', 'deSolve', 'gdata', 'gplots', 'gtools', 'kernlab', 'mvtnorm', 'permute', 'psych', 'quantmod', 'randomForest', 'rJava', 'R.matlab', 'R.methodsS3', 'ROCR', 'R.oo', 'R.utils', 'TTR', 'vegan', 'zoo', 'gdata', 'gplots', 'gtools', 'class', 'foreign', 'MASS', 'nlme', 'nnet', 'spatial' Update all/some/none? [a/s/n]: n Warning message: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘mzR’ had non-zero exit status

sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie)

locale: [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C [3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8 [5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8 [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] BiocInstaller_1.19.14

loaded via a namespace (and not attached): [1] tools_3.2.2

bbdamodaran commented 8 years ago

Kindly please see the following the information.

biocLite("mzR") BioC_mirror: https://bioconductor.org Using Bioconductor 3.2 (BiocInstaller 1.19.14), R 3.2.2 (2015-08-14). Installing package(s) ‘mzR’ essai de l'URL ' https://bioconductor.org/packages/3.2/bioc/src/contrib/mzR_2.3.2.tar.gz'

Content type 'application/x-gzip' length 14656653 bytes (14.0 MB)

downloaded 14.0 MB

The downloaded source packages are in ‘/tmp/Rtmpoe9gSB/downloaded_packages’ Old packages: 'abind', 'caTools', 'clue', 'deSolve', 'gdata', 'gplots', 'gtools', 'kernlab', 'mvtnorm', 'permute', 'psych', 'quantmod', 'randomForest', 'rJava', 'R.matlab', 'R.methodsS3', 'ROCR', 'R.oo', 'R.utils', 'TTR', 'vegan', 'zoo', 'gdata', 'gplots', 'gtools', 'class', 'foreign', 'MASS', 'nlme', 'nnet', 'spatial' Update all/some/none? [a/s/n]: n Warning message: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘mzR’ had non-zero exit status

sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie)

locale: [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C [3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8 [5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8 [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] BiocInstaller_1.19.14

loaded via a namespace (and not attached): [1] tools_3.2.2

ectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/Bina

Thanks

Bharath Bhushan D Post Doctoral Fellow IRISA-UBS, Vannes France

On Mon, Sep 21, 2015 at 4:58 PM, Sebastian Gibb notifications@github.com wrote:

Could you please provide the complete output of:

source("http://bioconductor.org/biocLite.R") biocLite("mzR")

and

sessionInfo()

— Reply to this email directly or view it on GitHub https://github.com/lgatto/MSnbase/issues/62#issuecomment-142007138.

sgibb commented 8 years ago

I assume you are missing the NetCDF libraries. Try to install the corresponding development files via su -c "apt-get install libnetcdf-dev" or sudo apt-get install libnetcdf-dev

bbdamodaran commented 8 years ago

Thank you for your information. After the installation of NetCDF libraries, I am able to install MSnbase package..

However, I have problem in installing "pRoloc" Package. Please see the below information for your reference

---------------------------------------------------
 biocLite("pRoloc")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.19.14), R 3.2.2 (2015-08-14).
Installing package(s) ‘pRoloc’
also installing the dependencies ‘rgl’, ‘RCurl’, ‘MLInterfaces’, ‘biomaRt’

essai de l'URL 'https://cran.rstudio.com/src/contrib/rgl_0.95.1337.tar.gz'
Content type 'application/x-gzip' length 2189241 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

essai de l'URL 'https://cran.rstudio.com/src/contrib/RCurl_1.95-4.7.tar.gz'
Content type 'application/x-gzip' length 916897 bytes (895 KB)
==================================================
downloaded 895 KB

essai de l'URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/MLInterfaces_1.49.13.tar.gz'
Content type 'application/x-gzip' length 1064898 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

essai de l'URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/biomaRt_2.25.3.tar.gz'
Content type 'application/x-gzip' length 278237 bytes (271 KB)
==================================================
downloaded 271 KB

essai de l'URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/pRoloc_1.9.6.tar.gz'
Content type 'application/x-gzip' length 4861660 bytes (4.6 MB)
==================================================
downloaded 4.6 MB

* installing *source* package ‘rgl’ ...
** package ‘rgl’ correctement décompressé et sommes MD5 vérifiées
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc... (cached) gcc -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -std=gnu99 accepts -g... (cached) yes
checking for gcc -std=gnu99 option to accept ISO C89... (cached) none needed
checking whether __attribute__((visibility())) is supported... yes
checking whether gcc -std=gnu99 accepts -fvisibility... yes
checking whether  accepts -fvisibility... no
checking for libpng-config... yes
configure: using libpng-config
configure: using libpng dynamic linkage
checking for X... libraries , headers
checking GL/gl.h usability... yes
checking GL/gl.h presence... yes
checking for GL/gl.h... yes
checking GL/glu.h usability... no
checking GL/glu.h presence... no
checking for GL/glu.h... no
configure: error: missing required header GL/glu.h
ERROR: configuration failed for package ‘rgl’
* removing ‘/share/home/damodara/R/x86_64-pc-linux-gnu-library/3.2/rgl’
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ correctement décompressé et sommes MD5 vérifiées
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/share/home/damodara/R/x86_64-pc-linux-gnu-library/3.2/RCurl’
ERROR: dependency ‘rgl’ is not available for package ‘MLInterfaces’
* removing ‘/share/home/damodara/R/x86_64-pc-linux-gnu-library/3.2/MLInterfaces’
ERROR: dependency ‘RCurl’ is not available for package ‘biomaRt’
* removing ‘/share/home/damodara/R/x86_64-pc-linux-gnu-library/3.2/biomaRt’
ERROR: dependencies ‘MLInterfaces’, ‘biomaRt’ are not available for package ‘pRoloc’
* removing ‘/share/home/damodara/R/x86_64-pc-linux-gnu-library/3.2/pRoloc’

The downloaded source packages are in
        ‘/tmp/RtmpWJ70cf/downloaded_packages’
Old packages: 'abind', 'caTools', 'clue', 'deSolve', 'gdata', 'gplots',
  'gtools', 'kernlab', 'mvtnorm', 'permute', 'psych', 'quantmod',
  'randomForest', 'rJava', 'R.matlab', 'R.methodsS3', 'ROCR', 'R.oo',
  'R.utils', 'TTR', 'vegan', 'zoo', 'gdata', 'gplots', 'gtools', 'class',
  'foreign', 'MASS', 'nlme', 'nnet', 'spatial'
Update all/some/none? [a/s/n]: n
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘rgl’ 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 ‘MLInterfaces’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘biomaRt’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘pRoloc’ had non-zero exit status

-----------------------------------------------------------------------------------------
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] BiocInstaller_1.19.14 MSnbase_1.17.14       ProtGenerics_1.1.0
[4] BiocParallel_1.3.52   mzR_2.3.2             Rcpp_0.12.1
[7] Biobase_2.29.1        BiocGenerics_0.15.6

loaded via a namespace (and not attached):
 [1] futile.logger_1.4.1   plyr_1.8.3            iterators_1.0.7
 [4] futile.options_1.0.0  tools_3.2.2           zlibbioc_1.15.0
 [7] MALDIquant_1.13       digest_0.6.8          preprocessCore_1.31.0
[10] gtable_0.1.2          lattice_0.20-33       foreach_1.4.2
[13] proto_0.3-10          stringr_1.0.0         S4Vectors_0.7.18
[16] IRanges_2.3.21        stats4_3.2.2          grid_3.2.2
[19] impute_1.43.0         XML_3.98-1.3          limma_3.25.16
[22] ggplot2_1.0.1         reshape2_1.4.1        lambda.r_1.1.7
[25] magrittr_1.5          scales_0.3.0          pcaMethods_1.59.0
[28] codetools_0.2-14      MASS_7.3-44           mzID_1.7.1
[31] colorspace_1.2-6      stringi_0.5-5         affy_1.47.1
[34] munsell_0.4.2         doParallel_1.0.8      vsn_3.37.3
[37] affyio_1.39.0
>
*** installing help indices
*
lgatto commented 8 years ago

Similar problem as previously, but for other external dependencies. To address configure: error: missing required header GL/glu.h, I would look for libglu1-mesa-dev. You will also need libcurl to be able to install RCurl.

bbdamodaran commented 8 years ago

Thank you very much for your information. Finally it works now

lgatto commented 8 years ago

A few clarifications about the errors your observed.

The first dependency, libnetcdf, was required for the mzR package. mzR is a rather complex package, that provides access to various mass spectrometry data formats such as mzXML, mzML, mzIdentML, ... and netCDF. Being able to access data in these relies on (sometimes complex) external software. In your case, that software was a low-level library to parse netCDF files.

libcurl is used to send and receive message over the internet. The package that relies on it is biomaRt, a fantastic resource that allows us to query a great many biological repositories, called Biomarts.