Using the correct mode absolutely solves it. Apologies for not trying the obvious.
Cheers Joris On Thu, May 3, 2018 at 2:10 PM, Martin Morgan <martin.mor...@roswellpark.org > wrote: > > > On 05/02/2018 03:21 PM, Joris Meys 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&for >> mat=file&file=GSM907811%2ECEL%2Egz >> ", >> destfile = "GSM907811.CEL.gz") >> > > On windows, the 'mode' argument to download.file() needs to be "wb" (write > binary) for binary files. > > Martin > > >> 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 >> >> >> > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > -- 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
