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[Bioc-devel] failed to build BSgenome data package in R-2.13 alpha (2011-03027 r55091)

5 messages · Mao Jianfeng, Hervé Pagès

Original
Mao Jianfeng
# 
Dear Bioc-devel listers,

I would like to get your helps on building BSgenome data package in
R-2.13 alpha. I tried it for many times, but I always failed to do
that. While, it can be done in R-2.11.1 and R-2.12.1 with their
specific updated version of BSgenome library.

Thanks in advance.

Best,
Jian-Feng,

Here I show some INFO:

########################################
(1) command I used:
library(BSgenome)
forgeBSgenomeDataPkg("Araly1_seed")

########################################
(2) seed file I used:
Package: BSgenome.Alyrata.JGI.v1
Title: Arabidopsis lyrata full genome (JGI version V1.0)
Description: Arabidopsis lyrata 8x Release [project ID 4002920] as
provided by JGI ( snapshot from March 24, 2011) and stored in
Biostrings objects.
Version: 1.0
#Author at R: c(person("Jian-Feng","Mao", email = "jianfeng.mao at gmail.com"),
#           person("Ya-Long","Guo", email = "ya-long.guo at tuebingen.mpg.de"),
#            person("Detlef","Weigel", email = "weigel at tue.mpg.de"))
Author: Jian-Feng Mao, with contributions from Ya-Long Guo and Detlef Weigel
Maintainer: Jian-Feng Mao <jianfeng.mao at gmail.com>
#Depends: BSgenome
License: Artistic-2.0
organism: Arabidopsis lyrata
species: Arabidopsis lyrata
provider: JGI (http://www.jgi.doe.gov/) in collaboration with Lab of
Detlef Weigel (http://www.weigelworld.org/)
provider_version: Assembly V1.0
release_date: April 7, 2008
release_name: The Arabidopsis lyrata genome sequence assembly v1.0
source_url: http://gp-edge3.jgi-psf.org:1080/Araly1/Araly1.home.html
organism_biocview: Alyrata
BSgenomeObjname: Alyrata
seqnames: paste("chr",c(1:8, "M", "C_scaffold_373", "C_scaffold_546",
"C_scaffold_732", "C_scaffold_757", "C_scaffold_764",
"C_scaffold_885"), sep = "")
mseqnames: paste("scaffold_",
c(9:11,13:29,31:39,41,43,47,48,51:54,57:61,63:66,68,70:74,76:77,80,83:92,
	96:100,103,106,108:110,112:115,117:118,120:123,125:126,128:130,132:133,
	135:139,141:144,146,149,151:152,158:161,163:167,169:170,172:173,176:181,
	184:185,188:191,193,195:197,199,201,203,205:216,219:223,225:226,228:231,233:236,239:244,
	246:253,255,258:259,261:262,264:271,275,277:279,281,283:290,292:295,
	298:305,307,310:311,315,319:320,322:323,325,327,330,332,334:335,337,
	339:352,354:355,357:358,361,363:366,368,371,372,374:376,378:381,
	383:388,390,396:398,400:403,408:409,412:413,415:417,419,426:429,431,
	433,435:436,439,441,443,446,447,449,450,451,453,455,457,460:464,
	467:472,474,475,477,480:482,484:489,491:493,496,500,501,504,505,507,
	509:510,512,516,519,520,525,527,531,532,535,540,548,549,551,552,554,557,
	558,562,564,565,566,569,573,575,576,579,580,582,584,585,587:589,591,
	592,594,595,597,602:604,607,608,610,612,614,615:617,624:631,635,636:639,
	642,645,646,649,651,653,655,658,659,661:672,674:675,677:686,688,693:695,
	697,699:702,704:707,710,711,713,715,716,717,719,721,723,726,727,728,729,731,
	733,734,735,736,738,739,740,741,744,746,747,748,752,753,755,756,759,
	761:763,766,769,770:773,776,777,779:784,786:788,790,792,793,795:798,801,802,
	804,805,807,810:815,817,819,823,825,828:832,834,835,837,838,840,843,
	845,848,849,851:853,855,858,861:862,864:867,868,871,872,875,877:884,887,
	890,891,893:896,900:904,905,908,911,912,915,918:920,924,928,936:941,945,
	946,947,950,954,955,958,960:965,968,970,971,975:979,981:984,986,
	987,989:994,996,998:1001,1003,1005:1008,1010,1012,1014,1015,1017,
	1019:1022,1025,1029,1031:1034,1040,1041,1043,1044,1046,1048,1052:1054,
	1056:1058,1061,1064,1069,1070,1072,1074,1076,1078,1080,1082,1084:1087,
	1089:1091,1094:1097,1099,1102,1105,1106,1109,1111:1113,1116:1118), sep = "")
nmask_per_seq: 0
SrcDataFiles1: all the chr*.fa file from
http://genome.jgi-psf.org/Araly1/Araly1.download.ftp.html
        WARNING: This is where things are today (March 24, 2011) but is probably
        NOT aimed to be the permanent URL for the V1.0 snapshot of the genome.
        JGI might update the content of this folder in the future with a new
        snapshot and move the V1.0 snapshot to the OLD/ subfolder.
PkgExamples: Alyrata
        seqlengths(Alyrata)
        Alyrata$chr1  # same as Alyrata[["chr1"]]
seqs_srcdir: /Volumes/PENDRIVE/Alyr_wholegenome/Araly1_assembly_scaffolds
# masks_srcdir: /home/steve/Data/Masks_src
# AGAPSfiles_name: cflo_v3.3.fa.masked
########################################
(3) R-2.13 version and sessionInfo()
_
platform       x86_64-unknown-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status         alpha
major          2
minor          13.0
year           2011
month          03
day            27
svn rev        55091
language       R
version.string R version 2.13.0 alpha (2011-03-27 r55091)
R version 2.13.0 alpha (2011-03-27 r55091)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
 [1] GenomicFeatures_1.3.15 GGtools_3.9.69         ff_2.2-1
 [4] bit_1.1-6              org.Hs.eg.db_2.5.0     rtracklayer_1.11.12
 [7] RCurl_1.5-0            bitops_1.0-4.1         annotate_1.29.3
[10] AnnotationDbi_1.13.18  GGBase_3.11.10         RSQLite_0.9-4
[13] DBI_0.2-5              snpStats_1.1.13        Matrix_0.999375-48
[16] lattice_0.19-17        survival_2.36-5        Biobase_2.11.10
[19] BSgenome_1.19.5        GenomicRanges_1.3.29   Biostrings_2.19.17
[22] IRanges_1.9.28

loaded via a namespace (and not attached):
[1] biomaRt_2.7.1 grid_2.13.0   XML_3.2-0     xtable_1.5-6

###################################
(4) error I got from R 2.13.0
Creating package in ./BSgenome.Alyrata.JGI.v1
Saving 'seqlengths' object to compressed data file
'./BSgenome.Alyrata.JGI.v1/inst/extdata/seqlengths.rda'... Error in
gzfile(file, "wb") : cannot open the connection
In addition: Warning message:
In gzfile(file, "wb") :
 cannot open compressed file
'./BSgenome.Alyrata.JGI.v1/inst/extdata/seqlengths.rda', probable
reason 'No such file or directory'

##################################
(5) R-2.12.1 version and sessionInfo()
_
platform       x86_64-apple-darwin9.8.0
arch           x86_64
os             darwin9.8.0
system         x86_64, darwin9.8.0
status
major          2
minor          12.1
year           2010
month          12
day            16
svn rev        53855
language       R
version.string R version 2.12.1 (2010-12-16)
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/UTF-8/C/C/C/C

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

other attached packages:
[1] BSgenome_1.18.3     Biostrings_2.18.4   GenomicRanges_1.2.3
[4] IRanges_1.8.9

loaded via a namespace (and not attached):
[1] Biobase_2.10.0

 ######################################
(6) R-2.11.1 version and sessionInfo()
_
platform       x86_64-unknown-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status
major          2
minor          11.1
year           2010
month          05
day            31
svn rev        52157
language       R
version.string R version 2.11.1 (2010-05-31)
R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu

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

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

other attached packages:
[1] Biobase_2.8.0       BSgenome_1.16.5     Biostrings_2.16.9
[4] GenomicRanges_1.0.9 IRanges_1.6.17

loaded via a namespace (and not attached):
[1] tools_2.11.1
Hervé Pagès
# 
Hi Jian-Feng,

Because of a recent change in R 2.13, the BSgenome source tarball and
binaries that are in the BioC 2.8 repositories are broken.
We are working on a solution. An immediate workaround is that you install
BSgenome directly from our Subversion repository:

  svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BSgenome

  user name: readonly
  password: readonly

Then just install with R CMD INSTALL BSgenome/
Please do NOT try to build the source tarball first (with R CMD build
BSgenome) as this would produce a broken source tarball.

Sorry for the inconvenience.

Cheers,
H.


----- Original Message -----
From: "Mao Jianfeng" <jianfeng.mao at gmail.com>
To: bioc-devel at r-project.org
Sent: Tuesday, March 29, 2011 6:29:20 AM
Subject: [Bioc-devel] failed to build BSgenome data package in R-2.13 alpha	(2011-03027 r55091)

Dear Bioc-devel listers,

I would like to get your helps on building BSgenome data package in
R-2.13 alpha. I tried it for many times, but I always failed to do
that. While, it can be done in R-2.11.1 and R-2.12.1 with their
specific updated version of BSgenome library.

Thanks in advance.

Best,
Jian-Feng,

Here I show some INFO:

########################################
(1) command I used:
library(BSgenome)
forgeBSgenomeDataPkg("Araly1_seed")

########################################
(2) seed file I used:
Package: BSgenome.Alyrata.JGI.v1
Title: Arabidopsis lyrata full genome (JGI version V1.0)
Description: Arabidopsis lyrata 8x Release [project ID 4002920] as
provided by JGI ( snapshot from March 24, 2011) and stored in
Biostrings objects.
Version: 1.0
#Author at R: c(person("Jian-Feng","Mao", email = "jianfeng.mao at gmail.com"),
#           person("Ya-Long","Guo", email = "ya-long.guo at tuebingen.mpg.de"),
#            person("Detlef","Weigel", email = "weigel at tue.mpg.de"))
Author: Jian-Feng Mao, with contributions from Ya-Long Guo and Detlef Weigel
Maintainer: Jian-Feng Mao <jianfeng.mao at gmail.com>
#Depends: BSgenome
License: Artistic-2.0
organism: Arabidopsis lyrata
species: Arabidopsis lyrata
provider: JGI (http://www.jgi.doe.gov/) in collaboration with Lab of
Detlef Weigel (http://www.weigelworld.org/)
provider_version: Assembly V1.0
release_date: April 7, 2008
release_name: The Arabidopsis lyrata genome sequence assembly v1.0
source_url: http://gp-edge3.jgi-psf.org:1080/Araly1/Araly1.home.html
organism_biocview: Alyrata
BSgenomeObjname: Alyrata
seqnames: paste("chr",c(1:8, "M", "C_scaffold_373", "C_scaffold_546",
"C_scaffold_732", "C_scaffold_757", "C_scaffold_764",
"C_scaffold_885"), sep = "")
mseqnames: paste("scaffold_",
c(9:11,13:29,31:39,41,43,47,48,51:54,57:61,63:66,68,70:74,76:77,80,83:92,
	96:100,103,106,108:110,112:115,117:118,120:123,125:126,128:130,132:133,
	135:139,141:144,146,149,151:152,158:161,163:167,169:170,172:173,176:181,
	184:185,188:191,193,195:197,199,201,203,205:216,219:223,225:226,228:231,233:236,239:244,
	246:253,255,258:259,261:262,264:271,275,277:279,281,283:290,292:295,
	298:305,307,310:311,315,319:320,322:323,325,327,330,332,334:335,337,
	339:352,354:355,357:358,361,363:366,368,371,372,374:376,378:381,
	383:388,390,396:398,400:403,408:409,412:413,415:417,419,426:429,431,
	433,435:436,439,441,443,446,447,449,450,451,453,455,457,460:464,
	467:472,474,475,477,480:482,484:489,491:493,496,500,501,504,505,507,
	509:510,512,516,519,520,525,527,531,532,535,540,548,549,551,552,554,557,
	558,562,564,565,566,569,573,575,576,579,580,582,584,585,587:589,591,
	592,594,595,597,602:604,607,608,610,612,614,615:617,624:631,635,636:639,
	642,645,646,649,651,653,655,658,659,661:672,674:675,677:686,688,693:695,
	697,699:702,704:707,710,711,713,715,716,717,719,721,723,726,727,728,729,731,
	733,734,735,736,738,739,740,741,744,746,747,748,752,753,755,756,759,
	761:763,766,769,770:773,776,777,779:784,786:788,790,792,793,795:798,801,802,
	804,805,807,810:815,817,819,823,825,828:832,834,835,837,838,840,843,
	845,848,849,851:853,855,858,861:862,864:867,868,871,872,875,877:884,887,
	890,891,893:896,900:904,905,908,911,912,915,918:920,924,928,936:941,945,
	946,947,950,954,955,958,960:965,968,970,971,975:979,981:984,986,
	987,989:994,996,998:1001,1003,1005:1008,1010,1012,1014,1015,1017,
	1019:1022,1025,1029,1031:1034,1040,1041,1043,1044,1046,1048,1052:1054,
	1056:1058,1061,1064,1069,1070,1072,1074,1076,1078,1080,1082,1084:1087,
	1089:1091,1094:1097,1099,1102,1105,1106,1109,1111:1113,1116:1118), sep = "")
nmask_per_seq: 0
SrcDataFiles1: all the chr*.fa file from
http://genome.jgi-psf.org/Araly1/Araly1.download.ftp.html
        WARNING: This is where things are today (March 24, 2011) but is probably
        NOT aimed to be the permanent URL for the V1.0 snapshot of the genome.
        JGI might update the content of this folder in the future with a new
        snapshot and move the V1.0 snapshot to the OLD/ subfolder.
PkgExamples: Alyrata
        seqlengths(Alyrata)
        Alyrata$chr1  # same as Alyrata[["chr1"]]
seqs_srcdir: /Volumes/PENDRIVE/Alyr_wholegenome/Araly1_assembly_scaffolds
# masks_srcdir: /home/steve/Data/Masks_src
# AGAPSfiles_name: cflo_v3.3.fa.masked
########################################
(3) R-2.13 version and sessionInfo()
_
platform       x86_64-unknown-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status         alpha
major          2
minor          13.0
year           2011
month          03
day            27
svn rev        55091
language       R
version.string R version 2.13.0 alpha (2011-03-27 r55091)
R version 2.13.0 alpha (2011-03-27 r55091)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
 [1] GenomicFeatures_1.3.15 GGtools_3.9.69         ff_2.2-1
 [4] bit_1.1-6              org.Hs.eg.db_2.5.0     rtracklayer_1.11.12
 [7] RCurl_1.5-0            bitops_1.0-4.1         annotate_1.29.3
[10] AnnotationDbi_1.13.18  GGBase_3.11.10         RSQLite_0.9-4
[13] DBI_0.2-5              snpStats_1.1.13        Matrix_0.999375-48
[16] lattice_0.19-17        survival_2.36-5        Biobase_2.11.10
[19] BSgenome_1.19.5        GenomicRanges_1.3.29   Biostrings_2.19.17
[22] IRanges_1.9.28

loaded via a namespace (and not attached):
[1] biomaRt_2.7.1 grid_2.13.0   XML_3.2-0     xtable_1.5-6

###################################
(4) error I got from R 2.13.0
Creating package in ./BSgenome.Alyrata.JGI.v1
Saving 'seqlengths' object to compressed data file
'./BSgenome.Alyrata.JGI.v1/inst/extdata/seqlengths.rda'... Error in
gzfile(file, "wb") : cannot open the connection
In addition: Warning message:
In gzfile(file, "wb") :
 cannot open compressed file
'./BSgenome.Alyrata.JGI.v1/inst/extdata/seqlengths.rda', probable
reason 'No such file or directory'

##################################
(5) R-2.12.1 version and sessionInfo()
_
platform       x86_64-apple-darwin9.8.0
arch           x86_64
os             darwin9.8.0
system         x86_64, darwin9.8.0
status
major          2
minor          12.1
year           2010
month          12
day            16
svn rev        53855
language       R
version.string R version 2.12.1 (2010-12-16)
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/UTF-8/C/C/C/C

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

other attached packages:
[1] BSgenome_1.18.3     Biostrings_2.18.4   GenomicRanges_1.2.3
[4] IRanges_1.8.9

loaded via a namespace (and not attached):
[1] Biobase_2.10.0

 ######################################
(6) R-2.11.1 version and sessionInfo()
_
platform       x86_64-unknown-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status
major          2
minor          11.1
year           2010
month          05
day            31
svn rev        52157
language       R
version.string R version 2.11.1 (2010-05-31)
R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu

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

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

other attached packages:
[1] Biobase_2.8.0       BSgenome_1.16.5     Biostrings_2.16.9
[4] GenomicRanges_1.0.9 IRanges_1.6.17

loaded via a namespace (and not attached):
[1] tools_2.11.1

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Mao Jianfeng
# 
Dear Pages,

Thanks for your helps and directions.

I did what you have showed me. But, it did not work for me.

I show you the INFO of my failing. I am feeling sorry for my troubles
to you. If the compatibility of BSgenome with R-2.13.0 can be worked
out soon by you. I just want to wait for that.

Thanks a lot.

Jian-Feng,

#########################################
(1) command and the return

$ R CMD INSTALL BSgenome/ --library=/ebio/abt6/jmao/bin/R-2.13/Rpacks
* installing *source* package ?BSgenome? ...
** R
** inst
** preparing package for lazy loading
Warning: package 'IRanges' was built under R version 2.13.0
Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
  Undefined subclass, "activeBindingFunction", of class
"expressionORfunction"; definition not updated
Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
  Undefined subclass, "refMethodDef", of class "expressionORfunction";
definition not updated
Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
  Undefined subclass, "defaultBindingFunction", of class
"expressionORfunction"; definition not updated
Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
  Undefined subclass, "activeBindingFunction", of class
"functionORNULL"; definition not updated
Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
  Undefined subclass, "refMethodDef", of class "functionORNULL";
definition not updated
Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
  Undefined subclass, "defaultBindingFunction", of class
"functionORNULL"; definition not updated
Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
  Undefined subclass, "namedList", of class "vectorORfactor";
definition not updated
Warning in .recacheSubclasses(def at className, def, doSubclasses, env) :
  Undefined subclass, "listOfMethods", of class "vectorORfactor";
definition not updated

Attaching package: 'IRanges'


	The following object(s) are masked from package:base :

	 Map,
	 cbind,
	 eval,
	 intersect,
	 mapply,
	 order,
	 paste,
	 pmax,
	 pmax.int,
	 pmin,
	 pmin.int,
	 rbind,
	 rep.int,
	 setdiff,
	 table,
	 union

Warning: package 'GenomicRanges' was built under R version 2.13.0
Error in sub("([^-]+)_.*", "\\1", info$pkgname) :
  7 arguments passed to .Internal(sub) which requires 8
Error : unable to load R code in package 'GenomicRanges'
Error : package 'GenomicRanges' could not be loaded
ERROR: lazy loading failed for package ?BSgenome?
* removing ?/ebio/abt6/jmao/bin/R-2.13/Rpacks/BSgenome?
* restoring previous ?/ebio/abt6/jmao/bin/R-2.13/Rpacks/BSgenome?

#########################################
(2) my R version and GenomicRanges library
_
platform       x86_64-unknown-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status         alpha
major          2
minor          13.0
year           2011
month          03
day            27
svn rev        55091
language       R
version.string R version 2.13.0 alpha (2011-03-27 r55091)
R version 2.13.0 alpha (2011-03-27 r55091)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] GenomicRanges_1.3.29 IRanges_1.9.28

loaded via a namespace (and not attached):
[1] tools_2.13.0
Hervé Pagès
# 
Hi Jian-Feng,

Seems like you have some version mismatch issues. Make sure that the R
you use when doing R CMD INSTALL is the one that was used for installing
all the stuff you have under /ebio/abt6/jmao/bin/R-2.13/Rpacks. In
particular, it should be R 2.13.

You can check this with 'which R', or just start 'R' and check the
version. If that's not the R you want, then use something like:

   /full/path/to/my/R CMD INSTALL BSgenome/ 
--library=/ebio/abt6/jmao/bin/R-2.13/Rpacks

Let me know if that's still not working.

H.
On 03/30/2011 02:17 AM, Mao Jianfeng wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Mao Jianfeng
    

    

      
      #
    

  


  

      
2011/3/30 Herv? Pag?s <hpages at fhcrc.org>:

            

      
      
      
    

        
It works for me, Thanks a lot.