[Bioc-devel] failed to build BSgenome data package in R-2.13 alpha (2011-03027 r55091)
Pages, Herve
hpages at fhcrc.org
Wed Mar 30 09:25:31 CEST 2011
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()
> version
_
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)
> sessionInfo()
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
> forgeBSgenomeDataPkg("Araly1_seed") # here the path of the seed file
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()
> version
_
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)
> sessionInfo()
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()
> version
_
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)
> sessionInfo()
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
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