GEOquery problem
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David ▴ 860
@david-3335
Last seen 6.7 years ago
It looks to me that there might some problem with softfiles. Did anybody came across a similar problem ?? library(GEOquery) gse <- getGEO(filename = system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery")) Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : invalid 'nlines' argument In addition: Warning messages: 1: In file(fname, "r") : file("") only supports open = "w+" and open = "w+b": using the former 2: In file(con, "r") : file("") only supports open = "w+" and open = "w+b": using the former 3: In file(fname, "r") : file("") only supports open = "w+" and open = "w+b": using the former
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@james-w-macdonald-5106
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Hi David, David martin wrote: > It looks to me that there might some problem with softfiles. Did anybody > came across a similar problem ?? > > > library(GEOquery) > gse <- getGEO(filename = > system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery")) > > Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : > invalid 'nlines' argument > In addition: Warning messages: > 1: In file(fname, "r") : > file("") only supports open = "w+" and open = "w+b": using the former > 2: In file(con, "r") : > file("") only supports open = "w+" and open = "w+b": using the former > 3: In file(fname, "r") : > file("") only supports open = "w+" and open = "w+b": using the former You have to point to a file that actually exists! > system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery") [1] "" If I use the softfile in that directory, it works for me. > gse <- getGEO(filename = system.file("extdata/GSE781_family.soft.gz",package = "GEOquery"), GSEMatrix=FALSE) Parsing.... Found 36 entities... GPL96 (1 of 36 entities) GPL97 (2 of 36 entities) GSM11805 (3 of 36 entities) GSM11810 (4 of 36 entities) GSM11814 (5 of 36 entities) GSM11815 (6 of 36 entities) GSM11823 (7 of 36 entities) GSM11827 (8 of 36 entities) GSM11830 (9 of 36 entities) GSM11832 (10 of 36 entities) GSM12067 (11 of 36 entities) GSM12069 (12 of 36 entities) GSM12075 (13 of 36 entities) GSM12078 (14 of 36 entities) GSM12079 (15 of 36 entities) GSM12083 (16 of 36 entities) GSM12098 (17 of 36 entities) GSM12099 (18 of 36 entities) GSM12100 (19 of 36 entities) GSM12101 (20 of 36 entities) GSM12105 (21 of 36 entities) GSM12106 (22 of 36 entities) GSM12268 (23 of 36 entities) GSM12269 (24 of 36 entities) GSM12270 (25 of 36 entities) GSM12274 (26 of 36 entities) GSM12283 (27 of 36 entities) GSM12287 (28 of 36 entities) GSM12298 (29 of 36 entities) GSM12299 (30 of 36 entities) GSM12300 (31 of 36 entities) GSM12301 (32 of 36 entities) GSM12399 (33 of 36 entities) GSM12412 (34 of 36 entities) GSM12444 (35 of 36 entities) GSM12448 (36 of 36 entities) > sessionInfo() R version 2.11.0 Patched (2010-05-01 r51890) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 loaded via a namespace (and not attached): [1] tools_2.11.0 Best, Jim > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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On Wed, Jun 9, 2010 at 12:12 PM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > Hi David, > > > David martin wrote: > >> It looks to me that there might some problem with softfiles. Did anybody >> came across a similar problem ?? >> >> >> library(GEOquery) >> gse <- getGEO(filename = >> system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery")) >> >> Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : >> invalid 'nlines' argument >> In addition: Warning messages: >> 1: In file(fname, "r") : >> file("") only supports open = "w+" and open = "w+b": using the former >> 2: In file(con, "r") : >> file("") only supports open = "w+" and open = "w+b": using the former >> 3: In file(fname, "r") : >> file("") only supports open = "w+" and open = "w+b": using the former >> > > You have to point to a file that actually exists! > > That said, that is a pretty useless error message--I should probably try to be a bit more specific.... Sean > > > system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery") > [1] "" > > If I use the softfile in that directory, it works for me. > > > gse <- getGEO(filename = > system.file("extdata/GSE781_family.soft.gz",package = "GEOquery"), > GSEMatrix=FALSE) > Parsing.... > Found 36 entities... > GPL96 (1 of 36 entities) > GPL97 (2 of 36 entities) > GSM11805 (3 of 36 entities) > GSM11810 (4 of 36 entities) > GSM11814 (5 of 36 entities) > GSM11815 (6 of 36 entities) > GSM11823 (7 of 36 entities) > GSM11827 (8 of 36 entities) > GSM11830 (9 of 36 entities) > GSM11832 (10 of 36 entities) > GSM12067 (11 of 36 entities) > GSM12069 (12 of 36 entities) > GSM12075 (13 of 36 entities) > GSM12078 (14 of 36 entities) > GSM12079 (15 of 36 entities) > GSM12083 (16 of 36 entities) > GSM12098 (17 of 36 entities) > GSM12099 (18 of 36 entities) > GSM12100 (19 of 36 entities) > GSM12101 (20 of 36 entities) > GSM12105 (21 of 36 entities) > GSM12106 (22 of 36 entities) > GSM12268 (23 of 36 entities) > GSM12269 (24 of 36 entities) > GSM12270 (25 of 36 entities) > GSM12274 (26 of 36 entities) > GSM12283 (27 of 36 entities) > GSM12287 (28 of 36 entities) > GSM12298 (29 of 36 entities) > GSM12299 (30 of 36 entities) > GSM12300 (31 of 36 entities) > GSM12301 (32 of 36 entities) > GSM12399 (33 of 36 entities) > GSM12412 (34 of 36 entities) > GSM12444 (35 of 36 entities) > GSM12448 (36 of 36 entities) > > > sessionInfo() > R version 2.11.0 Patched (2010-05-01 r51890) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] tools_2.11.0 > > Best, > > Jim > > > > > >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Sean, Yes you're right, that was a problem with file location but i still have a problem, see log file below.... A turn around for me was: > library(GEOquery) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: RCurl Loading required package: bitops > data="extdata/GSE21630_family.soft.gz" > gse <- getGEO(filename=data,GSEMatrix=FALSE) Parsing.... Found 47 entities... GPL9250 (1 of 47 entities) Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input > sessionInfo() R version 2.11.0 (2010-04-22) i686-pc-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=ca_AD.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=ca_AD.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 > On 06/09/2010 06:12 PM, James W. MacDonald wrote: > Hi David, > > David martin wrote: >> It looks to me that there might some problem with softfiles. Did >> anybody came across a similar problem ?? >> >> >> library(GEOquery) >> gse <- getGEO(filename = >> system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery")) >> >> Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : >> invalid 'nlines' argument >> In addition: Warning messages: >> 1: In file(fname, "r") : >> file("") only supports open = "w+" and open = "w+b": using the former >> 2: In file(con, "r") : >> file("") only supports open = "w+" and open = "w+b": using the former >> 3: In file(fname, "r") : >> file("") only supports open = "w+" and open = "w+b": using the former > > You have to point to a file that actually exists! > > > system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery") > [1] "" > > If I use the softfile in that directory, it works for me. > > > gse <- getGEO(filename = > system.file("extdata/GSE781_family.soft.gz",package = "GEOquery"), > GSEMatrix=FALSE) > Parsing.... > Found 36 entities... > GPL96 (1 of 36 entities) > GPL97 (2 of 36 entities) > GSM11805 (3 of 36 entities) > GSM11810 (4 of 36 entities) > GSM11814 (5 of 36 entities) > GSM11815 (6 of 36 entities) > GSM11823 (7 of 36 entities) > GSM11827 (8 of 36 entities) > GSM11830 (9 of 36 entities) > GSM11832 (10 of 36 entities) > GSM12067 (11 of 36 entities) > GSM12069 (12 of 36 entities) > GSM12075 (13 of 36 entities) > GSM12078 (14 of 36 entities) > GSM12079 (15 of 36 entities) > GSM12083 (16 of 36 entities) > GSM12098 (17 of 36 entities) > GSM12099 (18 of 36 entities) > GSM12100 (19 of 36 entities) > GSM12101 (20 of 36 entities) > GSM12105 (21 of 36 entities) > GSM12106 (22 of 36 entities) > GSM12268 (23 of 36 entities) > GSM12269 (24 of 36 entities) > GSM12270 (25 of 36 entities) > GSM12274 (26 of 36 entities) > GSM12283 (27 of 36 entities) > GSM12287 (28 of 36 entities) > GSM12298 (29 of 36 entities) > GSM12299 (30 of 36 entities) > GSM12300 (31 of 36 entities) > GSM12301 (32 of 36 entities) > GSM12399 (33 of 36 entities) > GSM12412 (34 of 36 entities) > GSM12444 (35 of 36 entities) > GSM12448 (36 of 36 entities) > > > sessionInfo() > R version 2.11.0 Patched (2010-05-01 r51890) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] tools_2.11.0 > > Best, > > Jim > > > >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >
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On Thu, Jun 10, 2010 at 9:01 AM, David martin <vilanew@gmail.com> wrote: > Sean, > Yes you're right, that was a problem with file location but i still have a > problem, see log file below.... > > A turn around for me was: > > > library(GEOquery) > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: RCurl > Loading required package: bitops > > data="extdata/GSE21630_family.soft.gz" > > gse <- getGEO(filename=data,GSEMatrix=FALSE) > Parsing.... > Found 47 entities... > GPL9250 (1 of 47 entities) > Error in read.table(file = file, header = header, sep = sep, quote = quote, > : > no lines available in input > Hi, David. Yep. It's a bug. Thanks for the report. The change has been committed to the release and devel branches and should be available soon in the next day or so. If you need it sooner, you can checkout from svn. Sean > > sessionInfo() > R version 2.11.0 (2010-04-22) > i686-pc-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=ca_AD.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=ca_AD.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > other attached packages: > [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 > > > > > > > > > On 06/09/2010 06:12 PM, James W. MacDonald wrote: > >> Hi David, >> >> David martin wrote: >> >>> It looks to me that there might some problem with softfiles. Did >>> anybody came across a similar problem ?? >>> >>> >>> library(GEOquery) >>> gse <- getGEO(filename = >>> system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery")) >>> >>> Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : >>> invalid 'nlines' argument >>> In addition: Warning messages: >>> 1: In file(fname, "r") : >>> file("") only supports open = "w+" and open = "w+b": using the former >>> 2: In file(con, "r") : >>> file("") only supports open = "w+" and open = "w+b": using the former >>> 3: In file(fname, "r") : >>> file("") only supports open = "w+" and open = "w+b": using the former >>> >> >> You have to point to a file that actually exists! >> >> > system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery") >> [1] "" >> >> If I use the softfile in that directory, it works for me. >> >> > gse <- getGEO(filename = >> system.file("extdata/GSE781_family.soft.gz",package = "GEOquery"), >> GSEMatrix=FALSE) >> Parsing.... >> Found 36 entities... >> GPL96 (1 of 36 entities) >> GPL97 (2 of 36 entities) >> GSM11805 (3 of 36 entities) >> GSM11810 (4 of 36 entities) >> GSM11814 (5 of 36 entities) >> GSM11815 (6 of 36 entities) >> GSM11823 (7 of 36 entities) >> GSM11827 (8 of 36 entities) >> GSM11830 (9 of 36 entities) >> GSM11832 (10 of 36 entities) >> GSM12067 (11 of 36 entities) >> GSM12069 (12 of 36 entities) >> GSM12075 (13 of 36 entities) >> GSM12078 (14 of 36 entities) >> GSM12079 (15 of 36 entities) >> GSM12083 (16 of 36 entities) >> GSM12098 (17 of 36 entities) >> GSM12099 (18 of 36 entities) >> GSM12100 (19 of 36 entities) >> GSM12101 (20 of 36 entities) >> GSM12105 (21 of 36 entities) >> GSM12106 (22 of 36 entities) >> GSM12268 (23 of 36 entities) >> GSM12269 (24 of 36 entities) >> GSM12270 (25 of 36 entities) >> GSM12274 (26 of 36 entities) >> GSM12283 (27 of 36 entities) >> GSM12287 (28 of 36 entities) >> GSM12298 (29 of 36 entities) >> GSM12299 (30 of 36 entities) >> GSM12300 (31 of 36 entities) >> GSM12301 (32 of 36 entities) >> GSM12399 (33 of 36 entities) >> GSM12412 (34 of 36 entities) >> GSM12444 (35 of 36 entities) >> GSM12448 (36 of 36 entities) >> >> > sessionInfo() >> R version 2.11.0 Patched (2010-05-01 r51890) >> i386-pc-mingw32 >> >> locale: >> [1] LC_COLLATE=English_United States.1252 >> [2] LC_CTYPE=English_United States.1252 >> [3] LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 >> >> loaded via a namespace (and not attached): >> [1] tools_2.11.0 >> >> Best, >> >> Jim >> >> >> >> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Sean, I have upgraded to GEOquery 2.13.2 but the problem is still there ?? which version fixes that issue ? thanks On 06/10/2010 03:55 PM, Sean Davis wrote: > On Thu, Jun 10, 2010 at 9:01 AM, David martin<vilanew at="" gmail.com=""> wrote: > >> Sean, >> Yes you're right, that was a problem with file location but i still have a >> problem, see log file below.... >> >> A turn around for me was: >> >>> library(GEOquery) >> Loading required package: Biobase >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> Loading required package: RCurl >> Loading required package: bitops >>> data="extdata/GSE21630_family.soft.gz" >>> gse<- getGEO(filename=data,GSEMatrix=FALSE) >> Parsing.... >> Found 47 entities... >> GPL9250 (1 of 47 entities) >> Error in read.table(file = file, header = header, sep = sep, quote = quote, >> : >> no lines available in input >> > > Hi, David. > > Yep. It's a bug. Thanks for the report. The change has been committed to > the release and devel branches and should be available soon in the next day > or so. If you need it sooner, you can checkout from svn. > > Sean > > > >>> sessionInfo() >> R version 2.11.0 (2010-04-22) >> i686-pc-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=ca_AD.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=ca_AD.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> >> other attached packages: >> [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 >>> >> >> >> >> >> >> >> On 06/09/2010 06:12 PM, James W. MacDonald wrote: >> >>> Hi David, >>> >>> David martin wrote: >>> >>>> It looks to me that there might some problem with softfiles. Did >>>> anybody came across a similar problem ?? >>>> >>>> >>>> library(GEOquery) >>>> gse<- getGEO(filename = >>>> system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery")) >>>> >>>> Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : >>>> invalid 'nlines' argument >>>> In addition: Warning messages: >>>> 1: In file(fname, "r") : >>>> file("") only supports open = "w+" and open = "w+b": using the former >>>> 2: In file(con, "r") : >>>> file("") only supports open = "w+" and open = "w+b": using the former >>>> 3: In file(fname, "r") : >>>> file("") only supports open = "w+" and open = "w+b": using the former >>>> >>> >>> You have to point to a file that actually exists! >>> >>> > system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery") >>> [1] "" >>> >>> If I use the softfile in that directory, it works for me. >>> >>> > gse<- getGEO(filename = >>> system.file("extdata/GSE781_family.soft.gz",package = "GEOquery"), >>> GSEMatrix=FALSE) >>> Parsing.... >>> Found 36 entities... >>> GPL96 (1 of 36 entities) >>> GPL97 (2 of 36 entities) >>> GSM11805 (3 of 36 entities) >>> GSM11810 (4 of 36 entities) >>> GSM11814 (5 of 36 entities) >>> GSM11815 (6 of 36 entities) >>> GSM11823 (7 of 36 entities) >>> GSM11827 (8 of 36 entities) >>> GSM11830 (9 of 36 entities) >>> GSM11832 (10 of 36 entities) >>> GSM12067 (11 of 36 entities) >>> GSM12069 (12 of 36 entities) >>> GSM12075 (13 of 36 entities) >>> GSM12078 (14 of 36 entities) >>> GSM12079 (15 of 36 entities) >>> GSM12083 (16 of 36 entities) >>> GSM12098 (17 of 36 entities) >>> GSM12099 (18 of 36 entities) >>> GSM12100 (19 of 36 entities) >>> GSM12101 (20 of 36 entities) >>> GSM12105 (21 of 36 entities) >>> GSM12106 (22 of 36 entities) >>> GSM12268 (23 of 36 entities) >>> GSM12269 (24 of 36 entities) >>> GSM12270 (25 of 36 entities) >>> GSM12274 (26 of 36 entities) >>> GSM12283 (27 of 36 entities) >>> GSM12287 (28 of 36 entities) >>> GSM12298 (29 of 36 entities) >>> GSM12299 (30 of 36 entities) >>> GSM12300 (31 of 36 entities) >>> GSM12301 (32 of 36 entities) >>> GSM12399 (33 of 36 entities) >>> GSM12412 (34 of 36 entities) >>> GSM12444 (35 of 36 entities) >>> GSM12448 (36 of 36 entities) >>> >>> > sessionInfo() >>> R version 2.11.0 Patched (2010-05-01 r51890) >>> i386-pc-mingw32 >>> >>> locale: >>> [1] LC_COLLATE=English_United States.1252 >>> [2] LC_CTYPE=English_United States.1252 >>> [3] LC_MONETARY=English_United States.1252 >>> [4] LC_NUMERIC=C >>> [5] LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] stats graphics grDevices datasets utils methods base >>> >>> other attached packages: >>> [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] tools_2.11.0 >>> >>> Best, >>> >>> Jim >>> >>> >>> >>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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On Mon, Jun 14, 2010 at 3:46 AM, David martin <vilanew@gmail.com> wrote: > Sean, > I have upgraded to GEOquery 2.13.2 but the problem is still there ?? which > version fixes that issue ? > > It is working for me. Do you mind some sessionInfo() and the exact code you are using? Thanks, Sean > gse = getGEO("GSE21630",GSEMatrix=FALSE) File stored at: /var/folders/F+/F+PwkbXqF6WeunvinD8pZk+++TI/-Tmp-//Rtmp1gPqTg/GSE21630 .soft Parsing.... Found 47 entities... GPL9250 (1 of 47 entities) GSM539835 (2 of 47 entities) .... GSM539879 (46 of 47 entities) GSM539880 (47 of 47 entities) > sessionInfo() R version 2.12.0 Under development (unstable) (2010-04-30 r51866) i386-apple-darwin9.8.0 locale: [1] en_US/en_US/C/C/en_US/en_US attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] GEOquery_2.13.2 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.9.0 loaded via a namespace (and not attached): [1] XML_3.1-0 > thanks > > > > On 06/10/2010 03:55 PM, Sean Davis wrote: > >> On Thu, Jun 10, 2010 at 9:01 AM, David martin<vilanew@gmail.com> wrote: >> >> Sean, >>> Yes you're right, that was a problem with file location but i still have >>> a >>> problem, see log file below.... >>> >>> A turn around for me was: >>> >>> library(GEOquery) >>>> >>> Loading required package: Biobase >>> >>> Welcome to Bioconductor >>> >>> Vignettes contain introductory material. To view, type >>> 'openVignette()'. To cite Bioconductor, see >>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>> >>> Loading required package: RCurl >>> Loading required package: bitops >>> >>>> data="extdata/GSE21630_family.soft.gz" >>>> gse<- getGEO(filename=data,GSEMatrix=FALSE) >>>> >>> Parsing.... >>> Found 47 entities... >>> GPL9250 (1 of 47 entities) >>> Error in read.table(file = file, header = header, sep = sep, quote = >>> quote, >>> : >>> no lines available in input >>> >>> >> Hi, David. >> >> Yep. It's a bug. Thanks for the report. The change has been committed >> to >> the release and devel branches and should be available soon in the next >> day >> or so. If you need it sooner, you can checkout from svn. >> >> Sean >> >> >> >> sessionInfo() >>>> >>> R version 2.11.0 (2010-04-22) >>> i686-pc-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=ca_AD.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=ca_AD.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> >>> other attached packages: >>> [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 >>> >>>> >>>> >>> >>> >>> >>> >>> >>> On 06/09/2010 06:12 PM, James W. MacDonald wrote: >>> >>> Hi David, >>>> >>>> David martin wrote: >>>> >>>> It looks to me that there might some problem with softfiles. Did >>>>> anybody came across a similar problem ?? >>>>> >>>>> >>>>> library(GEOquery) >>>>> gse<- getGEO(filename = >>>>> system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery")) >>>>> >>>>> Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : >>>>> invalid 'nlines' argument >>>>> In addition: Warning messages: >>>>> 1: In file(fname, "r") : >>>>> file("") only supports open = "w+" and open = "w+b": using the former >>>>> 2: In file(con, "r") : >>>>> file("") only supports open = "w+" and open = "w+b": using the former >>>>> 3: In file(fname, "r") : >>>>> file("") only supports open = "w+" and open = "w+b": using the former >>>>> >>>>> >>>> You have to point to a file that actually exists! >>>> >>>> > system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery") >>>> [1] "" >>>> >>>> If I use the softfile in that directory, it works for me. >>>> >>>> > gse<- getGEO(filename = >>>> system.file("extdata/GSE781_family.soft.gz",package = "GEOquery"), >>>> GSEMatrix=FALSE) >>>> Parsing.... >>>> Found 36 entities... >>>> GPL96 (1 of 36 entities) >>>> GPL97 (2 of 36 entities) >>>> GSM11805 (3 of 36 entities) >>>> GSM11810 (4 of 36 entities) >>>> GSM11814 (5 of 36 entities) >>>> GSM11815 (6 of 36 entities) >>>> GSM11823 (7 of 36 entities) >>>> GSM11827 (8 of 36 entities) >>>> GSM11830 (9 of 36 entities) >>>> GSM11832 (10 of 36 entities) >>>> GSM12067 (11 of 36 entities) >>>> GSM12069 (12 of 36 entities) >>>> GSM12075 (13 of 36 entities) >>>> GSM12078 (14 of 36 entities) >>>> GSM12079 (15 of 36 entities) >>>> GSM12083 (16 of 36 entities) >>>> GSM12098 (17 of 36 entities) >>>> GSM12099 (18 of 36 entities) >>>> GSM12100 (19 of 36 entities) >>>> GSM12101 (20 of 36 entities) >>>> GSM12105 (21 of 36 entities) >>>> GSM12106 (22 of 36 entities) >>>> GSM12268 (23 of 36 entities) >>>> GSM12269 (24 of 36 entities) >>>> GSM12270 (25 of 36 entities) >>>> GSM12274 (26 of 36 entities) >>>> GSM12283 (27 of 36 entities) >>>> GSM12287 (28 of 36 entities) >>>> GSM12298 (29 of 36 entities) >>>> GSM12299 (30 of 36 entities) >>>> GSM12300 (31 of 36 entities) >>>> GSM12301 (32 of 36 entities) >>>> GSM12399 (33 of 36 entities) >>>> GSM12412 (34 of 36 entities) >>>> GSM12444 (35 of 36 entities) >>>> GSM12448 (36 of 36 entities) >>>> >>>> > sessionInfo() >>>> R version 2.11.0 Patched (2010-05-01 r51890) >>>> i386-pc-mingw32 >>>> >>>> locale: >>>> [1] LC_COLLATE=English_United States.1252 >>>> [2] LC_CTYPE=English_United States.1252 >>>> [3] LC_MONETARY=English_United States.1252 >>>> [4] LC_NUMERIC=C >>>> [5] LC_TIME=English_United States.1252 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices datasets utils methods base >>>> >>>> other attached packages: >>>> [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] tools_2.11.0 >>>> >>>> Best, >>>> >>>> Jim >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>>> >>>> >>>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Sean, Here is the complete script. > library(GEOquery) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: RCurl Loading required package: bitops > > data="/home/dvi/extdata/GSE21630_family.soft.gz" > gse <- getGEO(filename=data,GSEMatrix=FALSE) Parsing.... Found 47 entities... GPL9250 (1 of 47 entities) Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GEOquery_2.13.2 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 On 06/14/2010 12:52 PM, Sean Davis wrote: > On Mon, Jun 14, 2010 at 3:46 AM, David martin<vilanew at="" gmail.com=""> wrote: > >> Sean, >> I have upgraded to GEOquery 2.13.2 but the problem is still there ?? which >> version fixes that issue ? >> >> > It is working for me. Do you mind some sessionInfo() and the exact code you > are using? > > Thanks, > Sean > >> gse = getGEO("GSE21630",GSEMatrix=FALSE) > File stored at: > /var/folders/F+/F+PwkbXqF6WeunvinD8pZk+++TI/-Tmp-//Rtmp1gPqTg/GSE216 30.soft > Parsing.... > Found 47 entities... > GPL9250 (1 of 47 entities) > GSM539835 (2 of 47 entities) > .... > GSM539879 (46 of 47 entities) > GSM539880 (47 of 47 entities) >> sessionInfo() > R version 2.12.0 Under development (unstable) (2010-04-30 r51866) > i386-apple-darwin9.8.0 > > locale: > [1] en_US/en_US/C/C/en_US/en_US > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] GEOquery_2.13.2 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.9.0 > > loaded via a namespace (and not attached): > [1] XML_3.1-0 > > > >> thanks >> >> >> >> On 06/10/2010 03:55 PM, Sean Davis wrote: >> >>> On Thu, Jun 10, 2010 at 9:01 AM, David martin<vilanew at="" gmail.com=""> wrote: >>> >>> Sean, >>>> Yes you're right, that was a problem with file location but i still have >>>> a >>>> problem, see log file below.... >>>> >>>> A turn around for me was: >>>> >>>> library(GEOquery) >>>>> >>>> Loading required package: Biobase >>>> >>>> Welcome to Bioconductor >>>> >>>> Vignettes contain introductory material. To view, type >>>> 'openVignette()'. To cite Bioconductor, see >>>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>>> >>>> Loading required package: RCurl >>>> Loading required package: bitops >>>> >>>>> data="extdata/GSE21630_family.soft.gz" >>>>> gse<- getGEO(filename=data,GSEMatrix=FALSE) >>>>> >>>> Parsing.... >>>> Found 47 entities... >>>> GPL9250 (1 of 47 entities) >>>> Error in read.table(file = file, header = header, sep = sep, quote = >>>> quote, >>>> : >>>> no lines available in input >>>> >>>> >>> Hi, David. >>> >>> Yep. It's a bug. Thanks for the report. The change has been committed >>> to >>> the release and devel branches and should be available soon in the next >>> day >>> or so. If you need it sooner, you can checkout from svn. >>> >>> Sean >>> >>> >>> >>> sessionInfo() >>>>> >>>> R version 2.11.0 (2010-04-22) >>>> i686-pc-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=ca_AD.UTF-8 LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=ca_AD.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> >>>> other attached packages: >>>> [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 >>>> >>>>> >>>>> >>>> >>>> >>>> >>>> >>>> >>>> On 06/09/2010 06:12 PM, James W. MacDonald wrote: >>>> >>>> Hi David, >>>>> >>>>> David martin wrote: >>>>> >>>>> It looks to me that there might some problem with softfiles. Did >>>>>> anybody came across a similar problem ?? >>>>>> >>>>>> >>>>>> library(GEOquery) >>>>>> gse<- getGEO(filename = >>>>>> system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery")) >>>>>> >>>>>> Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : >>>>>> invalid 'nlines' argument >>>>>> In addition: Warning messages: >>>>>> 1: In file(fname, "r") : >>>>>> file("") only supports open = "w+" and open = "w+b": using the former >>>>>> 2: In file(con, "r") : >>>>>> file("") only supports open = "w+" and open = "w+b": using the former >>>>>> 3: In file(fname, "r") : >>>>>> file("") only supports open = "w+" and open = "w+b": using the former >>>>>> >>>>>> >>>>> You have to point to a file that actually exists! >>>>> >>>>> > system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery") >>>>> [1] "" >>>>> >>>>> If I use the softfile in that directory, it works for me. >>>>> >>>>> > gse<- getGEO(filename = >>>>> system.file("extdata/GSE781_family.soft.gz",package = "GEOquery"), >>>>> GSEMatrix=FALSE) >>>>> Parsing.... >>>>> Found 36 entities... >>>>> GPL96 (1 of 36 entities) >>>>> GPL97 (2 of 36 entities) >>>>> GSM11805 (3 of 36 entities) >>>>> GSM11810 (4 of 36 entities) >>>>> GSM11814 (5 of 36 entities) >>>>> GSM11815 (6 of 36 entities) >>>>> GSM11823 (7 of 36 entities) >>>>> GSM11827 (8 of 36 entities) >>>>> GSM11830 (9 of 36 entities) >>>>> GSM11832 (10 of 36 entities) >>>>> GSM12067 (11 of 36 entities) >>>>> GSM12069 (12 of 36 entities) >>>>> GSM12075 (13 of 36 entities) >>>>> GSM12078 (14 of 36 entities) >>>>> GSM12079 (15 of 36 entities) >>>>> GSM12083 (16 of 36 entities) >>>>> GSM12098 (17 of 36 entities) >>>>> GSM12099 (18 of 36 entities) >>>>> GSM12100 (19 of 36 entities) >>>>> GSM12101 (20 of 36 entities) >>>>> GSM12105 (21 of 36 entities) >>>>> GSM12106 (22 of 36 entities) >>>>> GSM12268 (23 of 36 entities) >>>>> GSM12269 (24 of 36 entities) >>>>> GSM12270 (25 of 36 entities) >>>>> GSM12274 (26 of 36 entities) >>>>> GSM12283 (27 of 36 entities) >>>>> GSM12287 (28 of 36 entities) >>>>> GSM12298 (29 of 36 entities) >>>>> GSM12299 (30 of 36 entities) >>>>> GSM12300 (31 of 36 entities) >>>>> GSM12301 (32 of 36 entities) >>>>> GSM12399 (33 of 36 entities) >>>>> GSM12412 (34 of 36 entities) >>>>> GSM12444 (35 of 36 entities) >>>>> GSM12448 (36 of 36 entities) >>>>> >>>>> > sessionInfo() >>>>> R version 2.11.0 Patched (2010-05-01 r51890) >>>>> i386-pc-mingw32 >>>>> >>>>> locale: >>>>> [1] LC_COLLATE=English_United States.1252 >>>>> [2] LC_CTYPE=English_United States.1252 >>>>> [3] LC_MONETARY=English_United States.1252 >>>>> [4] LC_NUMERIC=C >>>>> [5] LC_TIME=English_United States.1252 >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices datasets utils methods base >>>>> >>>>> other attached packages: >>>>> [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] tools_2.11.0 >>>>> >>>>> Best, >>>>> >>>>> Jim >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at stat.math.ethz.ch >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>> [[alternative HTML version deleted]] >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Could that be because the soft file contains sequencing data instead of microarray data ? On 06/14/2010 02:20 PM, David martin wrote: > Sean, > Here is the complete script. > > > > library(GEOquery) > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: RCurl > Loading required package: bitops > > > > data="/home/dvi/extdata/GSE21630_family.soft.gz" > > gse <- getGEO(filename=data,GSEMatrix=FALSE) > Parsing.... > Found 47 entities... > GPL9250 (1 of 47 entities) > Error in read.table(file = file, header = header, sep = sep, quote = > quote, : > no lines available in input > > sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GEOquery_2.13.2 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 > > > > > > > > > > > On 06/14/2010 12:52 PM, Sean Davis wrote: >> On Mon, Jun 14, 2010 at 3:46 AM, David >> martin<vilanew at="" gmail.com=""> wrote: >> >>> Sean, >>> I have upgraded to GEOquery 2.13.2 but the problem is still there ?? >>> which >>> version fixes that issue ? >>> >>> >> It is working for me. Do you mind some sessionInfo() and the exact >> code you >> are using? >> >> Thanks, >> Sean >> >>> gse = getGEO("GSE21630",GSEMatrix=FALSE) >> File stored at: >> /var/folders/F+/F+PwkbXqF6WeunvinD8pZk+++TI/-Tmp-//Rtmp1gPqTg/GSE21 630.soft >> >> Parsing.... >> Found 47 entities... >> GPL9250 (1 of 47 entities) >> GSM539835 (2 of 47 entities) >> .... >> GSM539879 (46 of 47 entities) >> GSM539880 (47 of 47 entities) >>> sessionInfo() >> R version 2.12.0 Under development (unstable) (2010-04-30 r51866) >> i386-apple-darwin9.8.0 >> >> locale: >> [1] en_US/en_US/C/C/en_US/en_US >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] GEOquery_2.13.2 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.9.0 >> >> loaded via a namespace (and not attached): >> [1] XML_3.1-0 >> >> >> >>> thanks >>> >>> >>> >>> On 06/10/2010 03:55 PM, Sean Davis wrote: >>> >>>> On Thu, Jun 10, 2010 at 9:01 AM, David >>>> martin<vilanew at="" gmail.com=""> wrote: >>>> >>>> Sean, >>>>> Yes you're right, that was a problem with file location but i still >>>>> have >>>>> a >>>>> problem, see log file below.... >>>>> >>>>> A turn around for me was: >>>>> >>>>> library(GEOquery) >>>>>> >>>>> Loading required package: Biobase >>>>> >>>>> Welcome to Bioconductor >>>>> >>>>> Vignettes contain introductory material. To view, type >>>>> 'openVignette()'. To cite Bioconductor, see >>>>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>>>> >>>>> Loading required package: RCurl >>>>> Loading required package: bitops >>>>> >>>>>> data="extdata/GSE21630_family.soft.gz" >>>>>> gse<- getGEO(filename=data,GSEMatrix=FALSE) >>>>>> >>>>> Parsing.... >>>>> Found 47 entities... >>>>> GPL9250 (1 of 47 entities) >>>>> Error in read.table(file = file, header = header, sep = sep, quote = >>>>> quote, >>>>> : >>>>> no lines available in input >>>>> >>>>> >>>> Hi, David. >>>> >>>> Yep. It's a bug. Thanks for the report. The change has been committed >>>> to >>>> the release and devel branches and should be available soon in the next >>>> day >>>> or so. If you need it sooner, you can checkout from svn. >>>> >>>> Sean >>>> >>>> >>>> >>>> sessionInfo() >>>>>> >>>>> R version 2.11.0 (2010-04-22) >>>>> i686-pc-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=ca_AD.UTF-8 LC_NAME=C >>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=ca_AD.UTF-8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> >>>>> other attached packages: >>>>> [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 >>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 06/09/2010 06:12 PM, James W. MacDonald wrote: >>>>> >>>>> Hi David, >>>>>> >>>>>> David martin wrote: >>>>>> >>>>>> It looks to me that there might some problem with softfiles. Did >>>>>>> anybody came across a similar problem ?? >>>>>>> >>>>>>> >>>>>>> library(GEOquery) >>>>>>> gse<- getGEO(filename = >>>>>>> system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery")) >>>>>>> >>>>>>> Error in read.table(con, sep = "\t", header = FALSE, nrows = >>>>>>> nseries) : >>>>>>> invalid 'nlines' argument >>>>>>> In addition: Warning messages: >>>>>>> 1: In file(fname, "r") : >>>>>>> file("") only supports open = "w+" and open = "w+b": using the >>>>>>> former >>>>>>> 2: In file(con, "r") : >>>>>>> file("") only supports open = "w+" and open = "w+b": using the >>>>>>> former >>>>>>> 3: In file(fname, "r") : >>>>>>> file("") only supports open = "w+" and open = "w+b": using the >>>>>>> former >>>>>>> >>>>>>> >>>>>> You have to point to a file that actually exists! >>>>>> >>>>>> > system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery") >>>>>> [1] "" >>>>>> >>>>>> If I use the softfile in that directory, it works for me. >>>>>> >>>>>> > gse<- getGEO(filename = >>>>>> system.file("extdata/GSE781_family.soft.gz",package = "GEOquery"), >>>>>> GSEMatrix=FALSE) >>>>>> Parsing.... >>>>>> Found 36 entities... >>>>>> GPL96 (1 of 36 entities) >>>>>> GPL97 (2 of 36 entities) >>>>>> GSM11805 (3 of 36 entities) >>>>>> GSM11810 (4 of 36 entities) >>>>>> GSM11814 (5 of 36 entities) >>>>>> GSM11815 (6 of 36 entities) >>>>>> GSM11823 (7 of 36 entities) >>>>>> GSM11827 (8 of 36 entities) >>>>>> GSM11830 (9 of 36 entities) >>>>>> GSM11832 (10 of 36 entities) >>>>>> GSM12067 (11 of 36 entities) >>>>>> GSM12069 (12 of 36 entities) >>>>>> GSM12075 (13 of 36 entities) >>>>>> GSM12078 (14 of 36 entities) >>>>>> GSM12079 (15 of 36 entities) >>>>>> GSM12083 (16 of 36 entities) >>>>>> GSM12098 (17 of 36 entities) >>>>>> GSM12099 (18 of 36 entities) >>>>>> GSM12100 (19 of 36 entities) >>>>>> GSM12101 (20 of 36 entities) >>>>>> GSM12105 (21 of 36 entities) >>>>>> GSM12106 (22 of 36 entities) >>>>>> GSM12268 (23 of 36 entities) >>>>>> GSM12269 (24 of 36 entities) >>>>>> GSM12270 (25 of 36 entities) >>>>>> GSM12274 (26 of 36 entities) >>>>>> GSM12283 (27 of 36 entities) >>>>>> GSM12287 (28 of 36 entities) >>>>>> GSM12298 (29 of 36 entities) >>>>>> GSM12299 (30 of 36 entities) >>>>>> GSM12300 (31 of 36 entities) >>>>>> GSM12301 (32 of 36 entities) >>>>>> GSM12399 (33 of 36 entities) >>>>>> GSM12412 (34 of 36 entities) >>>>>> GSM12444 (35 of 36 entities) >>>>>> GSM12448 (36 of 36 entities) >>>>>> >>>>>> > sessionInfo() >>>>>> R version 2.11.0 Patched (2010-05-01 r51890) >>>>>> i386-pc-mingw32 >>>>>> >>>>>> locale: >>>>>> [1] LC_COLLATE=English_United States.1252 >>>>>> [2] LC_CTYPE=English_United States.1252 >>>>>> [3] LC_MONETARY=English_United States.1252 >>>>>> [4] LC_NUMERIC=C >>>>>> [5] LC_TIME=English_United States.1252 >>>>>> >>>>>> attached base packages: >>>>>> [1] stats graphics grDevices datasets utils methods base >>>>>> >>>>>> other attached packages: >>>>>> [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] tools_2.11.0 >>>>>> >>>>>> Best, >>>>>> >>>>>> Jim >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at stat.math.ethz.ch >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: >>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>> >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>>> >>>> [[alternative HTML version deleted]] >>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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On Mon, Jun 14, 2010 at 11:08 AM, David martin <vilanew@gmail.com> wrote: > Could that be because the soft file contains sequencing data instead of > microarray data ? > > Hi, David. Again, this is working for me, but using R-devel. The bug was in the platform parsing when the platform had no data table. Other than that, the processing is the same for sequencing and microarray data. I'll have to do a little more testing to see what might be different between my R-devel and R-2.11. Sorry for the inconvenience and thanks for the patience in helping me sort this out. Sean > > On 06/14/2010 02:20 PM, David martin wrote: > >> Sean, >> Here is the complete script. >> >> >> > library(GEOquery) >> Loading required package: Biobase >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> Loading required package: RCurl >> Loading required package: bitops >> > >> > data="/home/dvi/extdata/GSE21630_family.soft.gz" >> > gse <- getGEO(filename=data,GSEMatrix=FALSE) >> Parsing.... >> Found 47 entities... >> GPL9250 (1 of 47 entities) >> Error in read.table(file = file, header = header, sep = sep, quote = >> quote, : >> no lines available in input >> > sessionInfo() >> R version 2.11.1 (2010-05-31) >> x86_64-unknown-linux-gnu >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 >> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] GEOquery_2.13.2 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 >> >> >> >> >> >> >> >> >> >> >> On 06/14/2010 12:52 PM, Sean Davis wrote: >> >>> On Mon, Jun 14, 2010 at 3:46 AM, David >>> martin<vilanew@gmail.com> wrote: >>> >>> Sean, >>>> I have upgraded to GEOquery 2.13.2 but the problem is still there ?? >>>> which >>>> version fixes that issue ? >>>> >>>> >>>> It is working for me. Do you mind some sessionInfo() and the exact >>> code you >>> are using? >>> >>> Thanks, >>> Sean >>> >>> gse = getGEO("GSE21630",GSEMatrix=FALSE) >>>> >>> File stored at: >>> >>> /var/folders/F+/F+PwkbXqF6WeunvinD8pZk+++TI/-Tmp-//Rtmp1gPqTg/GSE2 1630.soft >>> >>> Parsing.... >>> Found 47 entities... >>> GPL9250 (1 of 47 entities) >>> GSM539835 (2 of 47 entities) >>> .... >>> GSM539879 (46 of 47 entities) >>> GSM539880 (47 of 47 entities) >>> >>>> sessionInfo() >>>> >>> R version 2.12.0 Under development (unstable) (2010-04-30 r51866) >>> i386-apple-darwin9.8.0 >>> >>> locale: >>> [1] en_US/en_US/C/C/en_US/en_US >>> >>> attached base packages: >>> [1] stats graphics grDevices datasets utils methods base >>> >>> other attached packages: >>> [1] GEOquery_2.13.2 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.9.0 >>> >>> loaded via a namespace (and not attached): >>> [1] XML_3.1-0 >>> >>> >>> >>> thanks >>>> >>>> >>>> >>>> On 06/10/2010 03:55 PM, Sean Davis wrote: >>>> >>>> On Thu, Jun 10, 2010 at 9:01 AM, David >>>>> martin<vilanew@gmail.com> wrote: >>>>> >>>>> Sean, >>>>> >>>>>> Yes you're right, that was a problem with file location but i still >>>>>> have >>>>>> a >>>>>> problem, see log file below.... >>>>>> >>>>>> A turn around for me was: >>>>>> >>>>>> library(GEOquery) >>>>>> >>>>>>> >>>>>>> Loading required package: Biobase >>>>>> >>>>>> Welcome to Bioconductor >>>>>> >>>>>> Vignettes contain introductory material. To view, type >>>>>> 'openVignette()'. To cite Bioconductor, see >>>>>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>>>>> >>>>>> Loading required package: RCurl >>>>>> Loading required package: bitops >>>>>> >>>>>> data="extdata/GSE21630_family.soft.gz" >>>>>>> gse<- getGEO(filename=data,GSEMatrix=FALSE) >>>>>>> >>>>>>> Parsing.... >>>>>> Found 47 entities... >>>>>> GPL9250 (1 of 47 entities) >>>>>> Error in read.table(file = file, header = header, sep = sep, quote = >>>>>> quote, >>>>>> : >>>>>> no lines available in input >>>>>> >>>>>> >>>>>> Hi, David. >>>>> >>>>> Yep. It's a bug. Thanks for the report. The change has been committed >>>>> to >>>>> the release and devel branches and should be available soon in the next >>>>> day >>>>> or so. If you need it sooner, you can checkout from svn. >>>>> >>>>> Sean >>>>> >>>>> >>>>> >>>>> sessionInfo() >>>>> >>>>>> >>>>>>> R version 2.11.0 (2010-04-22) >>>>>> i686-pc-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=ca_AD.UTF-8 LC_NAME=C >>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>>> [11] LC_MEASUREMENT=ca_AD.UTF-8 LC_IDENTIFICATION=C >>>>>> >>>>>> attached base packages: >>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>> >>>>>> >>>>>> other attached packages: >>>>>> [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 >>>>>> >>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 06/09/2010 06:12 PM, James W. MacDonald wrote: >>>>>> >>>>>> Hi David, >>>>>> >>>>>>> >>>>>>> David martin wrote: >>>>>>> >>>>>>> It looks to me that there might some problem with softfiles. Did >>>>>>> >>>>>>>> anybody came across a similar problem ?? >>>>>>>> >>>>>>>> >>>>>>>> library(GEOquery) >>>>>>>> gse<- getGEO(filename = >>>>>>>> system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery")) >>>>>>>> >>>>>>>> Error in read.table(con, sep = "\t", header = FALSE, nrows = >>>>>>>> nseries) : >>>>>>>> invalid 'nlines' argument >>>>>>>> In addition: Warning messages: >>>>>>>> 1: In file(fname, "r") : >>>>>>>> file("") only supports open = "w+" and open = "w+b": using the >>>>>>>> former >>>>>>>> 2: In file(con, "r") : >>>>>>>> file("") only supports open = "w+" and open = "w+b": using the >>>>>>>> former >>>>>>>> 3: In file(fname, "r") : >>>>>>>> file("") only supports open = "w+" and open = "w+b": using the >>>>>>>> former >>>>>>>> >>>>>>>> >>>>>>>> You have to point to a file that actually exists! >>>>>>> >>>>>>> > system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery") >>>>>>> [1] "" >>>>>>> >>>>>>> If I use the softfile in that directory, it works for me. >>>>>>> >>>>>>> > gse<- getGEO(filename = >>>>>>> system.file("extdata/GSE781_family.soft.gz",package = "GEOquery"), >>>>>>> GSEMatrix=FALSE) >>>>>>> Parsing.... >>>>>>> Found 36 entities... >>>>>>> GPL96 (1 of 36 entities) >>>>>>> GPL97 (2 of 36 entities) >>>>>>> GSM11805 (3 of 36 entities) >>>>>>> GSM11810 (4 of 36 entities) >>>>>>> GSM11814 (5 of 36 entities) >>>>>>> GSM11815 (6 of 36 entities) >>>>>>> GSM11823 (7 of 36 entities) >>>>>>> GSM11827 (8 of 36 entities) >>>>>>> GSM11830 (9 of 36 entities) >>>>>>> GSM11832 (10 of 36 entities) >>>>>>> GSM12067 (11 of 36 entities) >>>>>>> GSM12069 (12 of 36 entities) >>>>>>> GSM12075 (13 of 36 entities) >>>>>>> GSM12078 (14 of 36 entities) >>>>>>> GSM12079 (15 of 36 entities) >>>>>>> GSM12083 (16 of 36 entities) >>>>>>> GSM12098 (17 of 36 entities) >>>>>>> GSM12099 (18 of 36 entities) >>>>>>> GSM12100 (19 of 36 entities) >>>>>>> GSM12101 (20 of 36 entities) >>>>>>> GSM12105 (21 of 36 entities) >>>>>>> GSM12106 (22 of 36 entities) >>>>>>> GSM12268 (23 of 36 entities) >>>>>>> GSM12269 (24 of 36 entities) >>>>>>> GSM12270 (25 of 36 entities) >>>>>>> GSM12274 (26 of 36 entities) >>>>>>> GSM12283 (27 of 36 entities) >>>>>>> GSM12287 (28 of 36 entities) >>>>>>> GSM12298 (29 of 36 entities) >>>>>>> GSM12299 (30 of 36 entities) >>>>>>> GSM12300 (31 of 36 entities) >>>>>>> GSM12301 (32 of 36 entities) >>>>>>> GSM12399 (33 of 36 entities) >>>>>>> GSM12412 (34 of 36 entities) >>>>>>> GSM12444 (35 of 36 entities) >>>>>>> GSM12448 (36 of 36 entities) >>>>>>> >>>>>>> > sessionInfo() >>>>>>> R version 2.11.0 Patched (2010-05-01 r51890) >>>>>>> i386-pc-mingw32 >>>>>>> >>>>>>> locale: >>>>>>> [1] LC_COLLATE=English_United States.1252 >>>>>>> [2] LC_CTYPE=English_United States.1252 >>>>>>> [3] LC_MONETARY=English_United States.1252 >>>>>>> [4] LC_NUMERIC=C >>>>>>> [5] LC_TIME=English_United States.1252 >>>>>>> >>>>>>> attached base packages: >>>>>>> [1] stats graphics grDevices datasets utils methods base >>>>>>> >>>>>>> other attached packages: >>>>>>> [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0 >>>>>>> >>>>>>> loaded via a namespace (and not attached): >>>>>>> [1] tools_2.11.0 >>>>>>> >>>>>>> Best, >>>>>>> >>>>>>> Jim >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> >>>>>>>> Bioconductor mailing list >>>>>>>> Bioconductor@stat.math.ethz.ch >>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>> Search the archives: >>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> >>>>>> Bioconductor mailing list >>>>>> Bioconductor@stat.math.ethz.ch >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>>> >>>>>> [[alternative HTML version deleted]] >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>>> >>>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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