[R] Install bioconductor
David Hajage
dhajage.r at gmail.com
Sat Nov 11 20:43:35 CET 2006
Hello useRs,
I'm trying to install bioconductor on ubuntu edgy eft and R 2.4.0.
I have some error messages during installation, in particular for the
package "affy" :
"Error: package 'affy' required by 'makecdfenv' could not be found"
I have tryed to install 'makecdfenv' with the command :
getBioC("makecdfenv")
But I have this message :
Running getBioC version 0.1.8 with R version 2.4.0
Running biocinstall version 1.9.9 with R version 2.4.0
Your version of R requires version 1.9 of Bioconductor.
Avis dans install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
argument 'lib' is missing: using /usr/local/lib/R/site-library
also installing the dependencies 'affy', 'affyio'
essai de l'URL '
http://bioconductor.org/packages/1.9/bioc/src/contrib/affy_1.12.1.tar.gz'
Content type 'application/x-gzip' length 1370295 bytes
URL ouverte
==================================================
downloaded 1338Kb
essai de l'URL '
http://bioconductor.org/packages/1.9/bioc/src/contrib/affyio_1.2.0.tar.gz'
Content type 'application/x-gzip' length 57410 bytes
URL ouverte
==================================================
downloaded 56Kb
essai de l'URL '
http://bioconductor.org/packages/1.9/bioc/src/contrib/makecdfenv_1.12.0.tar.gz
'
Content type 'application/x-gzip' length 3222836 bytes
URL ouverte
==================================================
downloaded 3147Kb
* Installing *source* package 'affyio' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... no
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2
-std=gnu99 -c read_abatch.c -o read_abatch.o
read_abatch.c:151:18: error: zlib.h: Aucun fichier ou répertoire de ce type
read_abatch.c:1244: error: expected declaration specifiers or '...' before
'gzFile'
read_abatch.c: In function 'ReadgzFileLine':
read_abatch.c:1245: warning: implicit declaration of function 'gzgets'
read_abatch.c:1245: error: 'currentFile' undeclared (first use in this
function)
read_abatch.c:1245: error: (Each undeclared identifier is reported only once
read_abatch.c:1245: error: for each function it appears in.)
read_abatch.c:1245: warning: comparison between pointer and integer
read_abatch.c: At top level:
read_abatch.c:1265: error: expected '=', ',', ';', 'asm' or '__attribute__'
before 'open_gz_cel_file'
read_abatch.c:1306: error: expected ')' before 'my_file'
read_abatch.c:1329: error: expected ')' before 'my_file'
read_abatch.c: In function 'check_gzcel_file':
read_abatch.c:1360: error: 'gzFile' undeclared (first use in this function)
read_abatch.c:1360: error: expected ';' before 'currentFile'
read_abatch.c:1364: error: 'currentFile' undeclared (first use in this
function)
read_abatch.c:1364: warning: implicit declaration of function
'open_gz_cel_file'
read_abatch.c:1367: warning: implicit declaration of function
'gzAdvanceToSection'
read_abatch.c:1368: warning: implicit declaration of function
'gzfindStartsWith'
read_abatch.c:1393: warning: implicit declaration of function 'gzclose'
read_abatch.c: In function 'read_gzcel_file_intensities':
read_abatch.c:1421: error: 'gzFile' undeclared (first use in this function)
read_abatch.c:1421: error: expected ';' before 'currentFile'
read_abatch.c:1426: error: 'currentFile' undeclared (first use in this
function)
read_abatch.c:1432: error: too many arguments to function 'ReadgzFileLine'
read_abatch.c: In function 'read_gzcel_file_stddev':
read_abatch.c:1495: error: 'gzFile' undeclared (first use in this function)
read_abatch.c:1495: error: expected ';' before 'currentFile'
read_abatch.c:1500: error: 'currentFile' undeclared (first use in this
function)
read_abatch.c:1506: error: too many arguments to function 'ReadgzFileLine'
read_abatch.c: In function 'read_gzcel_file_npixels':
read_abatch.c:1579: error: 'gzFile' undeclared (first use in this function)
read_abatch.c:1579: error: expected ';' before 'currentFile'
read_abatch.c:1584: error: 'currentFile' undeclared (first use in this
function)
read_abatch.c:1590: error: too many arguments to function 'ReadgzFileLine'
read_abatch.c: In function 'gz_apply_masks':
read_abatch.c:1669: error: 'gzFile' undeclared (first use in this function)
read_abatch.c:1669: error: expected ';' before 'currentFile'
read_abatch.c:1678: error: 'currentFile' undeclared (first use in this
function)
read_abatch.c:1691: error: too many arguments to function 'ReadgzFileLine'
read_abatch.c:1715: error: too many arguments to function 'ReadgzFileLine'
read_abatch.c: In function 'gz_get_header_info':
read_abatch.c:1749: error: 'gzFile' undeclared (first use in this function)
read_abatch.c:1749: error: expected ';' before 'currentFile'
read_abatch.c:1753: error: 'currentFile' undeclared (first use in this
function)
read_abatch.c: In function 'gz_get_detailed_header_info':
read_abatch.c:1807: error: 'gzFile' undeclared (first use in this function)
read_abatch.c:1807: error: 'currentFile' undeclared (first use in this
function)
read_abatch.c: In function 'gz_get_masks_outliers':
read_abatch.c:1916: error: 'gzFile' undeclared (first use in this function)
read_abatch.c:1916: error: 'currentFile' undeclared (first use in this
function)
read_abatch.c:1941: error: too many arguments to function 'ReadgzFileLine'
read_abatch.c:1969: error: too many arguments to function 'ReadgzFileLine'
read_abatch.c: In function 'isgzTextCelFile':
read_abatch.c:2012: error: 'gzFile' undeclared (first use in this function)
read_abatch.c:2012: error: expected ';' before 'currentFile'
read_abatch.c:2014: error: 'currentFile' undeclared (first use in this
function)
read_abatch.c:2014: warning: implicit declaration of function 'gzopen'
read_abatch.c:2019: error: too many arguments to function 'ReadgzFileLine'
make: *** [read_abatch.o] Erreur 1
chmod: ne peut accéder `/usr/local/lib/R/site-library/affyio/libs/*': Aucun
fichier ou répertoire de ce type
ERROR: compilation failed for package 'affyio'
** Removing '/usr/local/lib/R/site-library/affyio'
* Installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... no
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2
-std=gnu99 -c chipbackground.c -o chipbackground.o
gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2
-std=gnu99 -c getall_locations.c -o getall_locations.o
gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2
-std=gnu99 -c mas5calls.c -o mas5calls.o
gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2
-std=gnu99 -c qnorm.c -o qnorm.o
gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2
-std=gnu99 -c rma2.c -o rma2.o
gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2
-std=gnu99 -c rma_background2.c -o rma_background2.o
gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2
-std=gnu99 -c rma_common.c -o rma_common.o
gcc -shared -o affy.so chipbackground.o getall_locations.o mas5calls.o
qnorm.o rma2.o rma_background2.o rma_common.o -L/usr/lib/R/lib -lR
** R
** data
** demo
** inst
** save image
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: affyio
Error: package 'affyio' could not be loaded
In addition: Warning message:
there is no package called 'affyio' in: library(pkg, character.only = TRUE,
logical = TRUE, lib.loc = lib.loc)
Execution halted
cat: erreur d'écriture: Relais brisé (pipe)
ERROR: execution of package source for 'affy' failed
** Removing '/usr/local/lib/R/site-library/affy'
* Installing *source* package 'makecdfenv' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... no
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2
-std=gnu99 -c read_cdffile.c -o read_cdffile.o
gcc -shared -o makecdfenv.so read_cdffile.o -L/usr/lib/R/lib -lR
** R
** inst
** save image
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Error: package 'affy' required by 'makecdfenv' could not be found
Execution halted
ERROR: execution of package source for 'makecdfenv' failed
** Removing '/usr/local/lib/R/site-library/makecdfenv'
The downloaded packages are in
/tmp/Rtmpjfx2Db/downloaded_packages
Warning messages:
1: installation of package 'affyio' had non-zero exit status in:
install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
2: installation of package 'affy' had non-zero exit status in:
install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
3: installation of package 'makecdfenv' had non-zero exit status in:
install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
>
How can fix this ?
Thank you for help.
David
More information about the R-help
mailing list