Use mode="wb" when you download the file. See https://github.com/HenrikBengtsson/Wishlist-for-R/issues/30.
R core, and others, is there a good argument for why we are not making this the default download mode? It seems like a such a simple fix to such a common "mistake". Henrik On Thu, May 3, 2018, 00:44 Joris Meys <jorism...@gmail.com> wrote: > Dear all, > > I've noticed by trying to download gz files from here : > https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM907811 > > At the bottom one can download GSM907811.CEL.gz . If I download this > manually and try > > oligo::read.celfiles("GSM907811.CEL.gz") > > everything works fine. (oligo is a bioConductor package) > > However, if I download using > > download.file(" > > https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM907811&format=file&file=GSM907811%2ECEL%2Egz > ", > destfile = "GSM907811.CEL.gz") > > The file is downloaded, but oligo::read.celfiles() returns the following > error: > > Error in checkChipTypes(filenames, verbose, "affymetrix", TRUE) : > End of gz file reached unexpectedly. Perhaps this file is truncated. > > Moreover, if I try to delete it after using download.file(), I get a > warning that permission is denied. I can only remove it using Windows file > explorer after I closed the R session, indicating that the connection is > still open. Yet, showConnections() doesn't show any open connections > either. > > Session info below. Note that I started from a completely fresh R session. > oligo is needed due to the specific file format of these gz files. They're > not standard tarred files. > > Cheers > Joris > > Session Info > > ------------------------------------------------------------------------------------- > > R version 3.5.0 (2018-04-23) > Platform: x86_64-w64-mingw32/x64 (64-bit) > Running under: Windows >= 8 x64 (build 9200) > > Matrix products: default > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United > Kingdom.1252 > [3] LC_MONETARY=English_United Kingdom.1252 > LC_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats4 parallel stats graphics grDevices utils datasets > methods > [9] base > > other attached packages: > [1] pd.hugene.1.0.st.v1_3.14.1 DBI_0.8 > oligo_1.44.0 > [4] Biobase_2.39.2 oligoClasses_1.42.0 > RSQLite_2.1.0 > [7] Biostrings_2.48.0 XVector_0.19.9 > IRanges_2.13.28 > [10] S4Vectors_0.17.42 BiocGenerics_0.25.3 > > loaded via a namespace (and not attached): > [1] Rcpp_0.12.16 compiler_3.5.0 > [3] BiocInstaller_1.30.0 GenomeInfoDb_1.15.5 > [5] bitops_1.0-6 iterators_1.0.9 > [7] tools_3.5.0 zlibbioc_1.25.0 > [9] digest_0.6.15 bit_1.1-12 > [11] memoise_1.1.0 preprocessCore_1.41.0 > [13] lattice_0.20-35 ff_2.2-13 > [15] pkgconfig_2.0.1 Matrix_1.2-14 > [17] foreach_1.4.4 DelayedArray_0.5.31 > [19] yaml_2.1.18 GenomeInfoDbData_1.1.0 > [21] affxparser_1.52.0 bit64_0.9-7 > [23] grid_3.5.0 BiocParallel_1.13.3 > [25] blob_1.1.1 codetools_0.2-15 > [27] matrixStats_0.53.1 GenomicRanges_1.31.23 > [29] splines_3.5.0 SummarizedExperiment_1.9.17 > [31] RCurl_1.95-4.10 affyio_1.49.2 > > > -- > Joris Meys > Statistical consultant > > Department of Data Analysis and Mathematical Modelling > Ghent University > Coupure Links 653, B-9000 Gent (Belgium) > < > https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium&entry=gmail&source=g > > > > ----------- > Biowiskundedagen 2017-2018 > http://www.biowiskundedagen.ugent.be/ > > ------------------------------- > Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
