These are warnings, not errors. You can safely ignore them. I'll work on silencing them as time permits. Sean On Wed, Aug 31, 2011 at 12:16 PM, zhliu.tju <zhliu.tju at="" gmail.com=""> wrote: > Hi Bioconductor users, > > I encounter a problem in library GEOquery, I downloaded soft format gene > expression profile from GEO database. > > whenever I run below lines, there appears a warning message though already > read in the soft file. > >> setwd("C:\\work\\microarray\\Implementation") >> GSE781<- getGEO(filename = "GSE781_family.soft.gz") > > There were 50 or more warnings (use warnings() to see the first 50) > > Warning messages: > 1: In readLines(con, 1) : seek on a gzfile connection returned an internal > error > 2: In readLines(con, 1) : seek on a gzfile connection returned an internal > error > 3: In readLines(con, 1) : seek on a gzfile connection returned an internal > error > 4: In readLines(con, 1) : seek on a gzfile connection returned an internal > error > 5: In readLines(con, 1) : seek on a gzfile connection returned an internal > error > 6: In readLines(con, 1) : seek on a gzfile connection returned an internal > error > >> sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 > [2] LC_CTYPE=English_United Kingdom.1252 > [3] LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] splines ? stats4 ? ?stats ? ? graphics ?grDevices utils ? ? datasets > [8] methods ? base > > other attached packages: > ?[1] annotate_1.30.0 ? ? ?affydata_1.11.11 ? ? affy_1.30.0 > ?[4] flexmix_2.3-5 ? ? ? ?multcomp_1.2-7 ? ? ? survival_2.36-9 > ?[7] mvtnorm_0.9-9991 ? ? modeltools_0.2-17 ? ?lattice_0.19-30 > [10] bioDist_1.24.1 ? ? ? KernSmooth_2.23-6 ? ?genefilter_1.34.0 > [13] hgu133a.db_2.5.0 ? ? org.Hs.eg.db_2.5.0 ? RSQLite_0.9-4 > [16] DBI_0.2-5 ? ? ? ? ? ?AnnotationDbi_1.14.1 reshape_0.8.4 > [19] plyr_1.6 ? ? ? ? ? ? GEOquery_2.19.3 ? ? ?Biobase_2.12.2 > > loaded via a namespace (and not attached): > [1] affyio_1.20.0 ? ? ? ? grid_2.13.1 ? ? ? ? ? preprocessCore_1.14.0 > [4] RCurl_1.6-7.1 ? ? ? ? tools_2.13.1 ? ? ? ? ?XML_3.4-2.2 > [7] xtable_1.5-6 > > Anyone knows how to deal with the above problems, thanks a lot in advance! > > -- > Best Regards, > > Zhe Liu > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >