Hi, I'm trying to figure out what is going wrong in https://support.bioconductor.org/p/93182/. Mustafa is using recount to load a bigwig file from the web. The code in recount relies on some code in derfinder, and the actual importing is done by rtracklayer::import().
>From looking at the R session information reported by Mustafa I can't tell what's wrong. He has the correct versions of rtracklayer, derfinder and recount installed. He also has openssl and pkg-config installed. At first I thought that he might be missing openssl since it's not listed as a SystemRequirement in the description file of rtracklayer/derfinder/recount. I looked back at https://support.bioconductor.org/p/81267/ and installed the latest openssl, made it available on my PATH and installed rtracklayer from SVN source on both R 3.4.0 and 3.3.2. In both situations, the R code worked for me despite the message "checking for OPENSSL... no" when installing rtracklayer. It used to be that it would say "yes" instead of no as you can see at https://support.bioconductor.org/p/81267/#82142. So, it doesn't look like it's a version issue with R packages. It's not a problem with either the latest openssl via homebrew or other versions https://support.bioconductor.org/p/93182/#93223. I doubt that it's an issue specific due to his openssl version (in between the older and newer versions I tested) or his pkg-util version. It's not an RStudio problem either (version 1.0.136 with both R 3.3.2 and 3.4.0). Could it be an RCurl issue? Could it be that his IP is blocked by the server hosting the BigWig file? Anyhow, I don't know what is the source of the problem and have not been able to reproduce it. Hopefully someone here has an idea of what is the problem. Best, Leo $ brew install --force openssl ## Edited by .bashrc with the following line: export PATH="/usr/local/opt/openssl/bin:$PATH" $ which openssl /usr/local/opt/openssl/bin/openssl $ openssl version OpenSSL 1.0.2k 26 Jan 2017 $ svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rtracklayer $ R CMD INSTALL rtracklayer Loading required package: colorout * installing to library ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’ * installing *source* package ‘rtracklayer’ ... checking for pkg-config... /usr/local/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for OPENSSL... no ... Then I was able to run without problems > library(rtracklayer) > x <- import.bw('http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw',as > = 'RleList') > x RleList of length 94 $chr1 numeric-Rle of length 248956422 with 1249470 runs Lengths: 13378 37 366 37 25 37 443 37 73 1 ... 24 13 24 2 37 535 37 1028 37 13595 Values : 0 1 0 1 0 1 0 1 0 1 ... 1 2 1 0 1 0 1 0 1 0 $chr10 numeric-Rle of length 133797422 with 412887 runs Lengths: 47132 37 12 37 333 1 3 3 1 1 ... 37 479 37 379 37 211 37 2082 37 11003 Values : 0 1 0 1 0 1 2 3 4 5 ... 1 0 1 0 1 0 1 0 1 0 $chr11 numeric-Rle of length 135086622 with 700940 runs Lengths: 74243 37 22178 37 22907 37 699 37 1236 ... 37 66776 37 36834 37 4395 37 17340 Values : 0 1 0 1 0 1 0 1 0 ... 1 0 1 0 1 0 1 0 $chr11_KI270721v1_random numeric-Rle of length 100316 with 363 runs Lengths: 2593 37 17 7 1 29 7 1 2364 37 ... 33 8048 37 172 37 876 37 492 37 47993 Values : 0 1 0 1 2 3 2 1 0 1 ... 1 0 1 0 1 0 1 0 1 0 $chr12 numeric-Rle of length 133275309 with 628862 runs Lengths: 10055 37 4101 37 316 10 1 1 4 21 ... 37 13 37 263 37 623 37 4860 37 64715 Values : 0 1 0 1 0 1 2 3 4 5 ... 1 0 1 0 1 0 1 0 1 0 ... <89 more elements> > options(width = 120) > devtools::session_info() Session info ----------------------------------------------------------------------------------------------------------- setting value version R Under development (unstable) (2016-10-26 r71594) system x86_64, darwin13.4.0 ui AQUA language (EN) collate en_US.UTF-8 tz America/New_York date 2017-03-01 Packages --------------------------------------------------------------------------------------------------------------- package * version date source Biobase 2.35.1 2017-02-23 Bioconductor BiocGenerics * 0.21.3 2017-01-12 Bioconductor BiocParallel 1.9.5 2017-01-24 Bioconductor Biostrings 2.43.4 2017-02-02 Bioconductor bitops 1.0-6 2013-08-17 CRAN (R 3.4.0) DelayedArray 0.1.7 2017-02-17 Bioconductor devtools 1.12.0 2016-12-05 CRAN (R 3.4.0) digest 0.6.12 2017-01-27 CRAN (R 3.4.0) GenomeInfoDb * 1.11.9 2017-02-08 Bioconductor GenomeInfoDbData 0.99.0 2017-02-14 Bioconductor GenomicAlignments 1.11.9 2017-02-02 Bioconductor GenomicRanges * 1.27.23 2017-02-25 Bioconductor IRanges * 2.9.18 2017-02-02 Bioconductor lattice 0.20-34 2016-09-06 CRAN (R 3.4.0) Matrix 1.2-8 2017-01-20 CRAN (R 3.4.0) matrixStats 0.51.0 2016-10-09 CRAN (R 3.4.0) memoise 1.0.0 2016-01-29 CRAN (R 3.4.0) RCurl 1.95-4.8 2016-03-01 CRAN (R 3.4.0) Rsamtools 1.27.12 2017-01-24 Bioconductor rtracklayer * 1.35.6 2017-03-01 Bioconductor S4Vectors * 0.13.15 2017-02-14 cran (@0.13.15) SummarizedExperiment 1.5.7 2017-02-23 Bioconductor withr 1.0.2 2016-06-20 CRAN (R 3.4.0) XML 3.98-1.5 2016-11-10 CRAN (R 3.4.0) XVector 0.15.2 2017-02-02 Bioconductor zlibbioc 1.21.0 2016-10-23 Bioconductor I had also just previously tried before updating my openssl: $ /usr/bin/openssl version OpenSSL 0.9.8zh 14 Jan 2016 Similarly, everything worked on my system with R 3.3.2 despite the pkg-config not finding openssl. $ R CMD INSTALL rtracklayer Loading required package: colorout * installing to library ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’ * installing *source* package ‘rtracklayer’ ... checking for pkg-config... /usr/local/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for OPENSSL... no ... > library(rtracklayer) > x <- import.bw('http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw',as > = 'RleList') > options(width = 120) > devtools::session_info() Session info ----------------------------------------------------------------------------------------------------------- setting value version R version 3.3.2 RC (2016-10-26 r71594) system x86_64, darwin13.4.0 ui X11 language (EN) collate en_US.UTF-8 tz America/New_York date 2017-03-01 Packages --------------------------------------------------------------------------------------------------------------- package * version date source Biobase 2.34.0 2016-10-18 Bioconductor BiocGenerics * 0.20.0 2016-10-18 Bioconductor BiocParallel 1.8.1 2016-10-30 Bioconductor Biostrings 2.42.1 2016-12-01 Bioconductor bitops 1.0-6 2013-08-17 cran (@1.0-6) colorout * 1.1-2 2016-10-19 Github (jalvesaq/colorout@6d84420) devtools 1.12.0 2016-06-24 CRAN (R 3.3.0) digest 0.6.12 2017-01-27 CRAN (R 3.3.2) GenomeInfoDb * 1.10.3 2017-02-07 Bioconductor GenomicAlignments 1.10.0 2016-10-18 Bioconductor GenomicRanges * 1.26.3 2017-02-25 Bioconductor IRanges * 2.8.1 2016-11-08 Bioconductor lattice 0.20-34 2016-09-06 CRAN (R 3.3.2) Matrix 1.2-8 2017-01-20 CRAN (R 3.3.2) memoise 1.0.0 2016-01-29 CRAN (R 3.3.0) RCurl 1.95-4.8 2016-03-01 cran (@1.95-4.) Rsamtools 1.26.1 2016-10-22 Bioconductor rtracklayer * 1.34.2 2017-03-01 Bioconductor S4Vectors * 0.12.1 2016-12-01 Bioconductor SummarizedExperiment 1.4.0 2016-10-18 Bioconductor withr 1.0.2 2016-06-20 CRAN (R 3.3.0) XML 3.98-1.5 2016-11-10 CRAN (R 3.3.2) XVector 0.14.0 2016-10-18 Bioconductor zlibbioc 1.20.0 2016-10-18 Bioconductor Back to R 3.4.0 showing the RCurl info: > library(RCurl) Loading required package: bitops > curlVersion() $age [1] 3 $version [1] "7.51.0" $vesion_num [1] 471808 $host [1] "x86_64-apple-darwin16.0" $features ipv6 ssl libz ntlm asynchdns spnego largefile ntlm_wb 1 4 8 16 128 256 512 32768 $ssl_version [1] "SecureTransport" $ssl_version_num [1] 0 $libz_version [1] "1.2.8" $protocols [1] "dict" "file" "ftp" "ftps" "gopher" "http" "https" "imap" "imaps" "ldap" "ldaps" "pop3" "pop3s" "rtsp" [15] "smb" "smbs" "smtp" "smtps" "telnet" "tftp" $ares [1] "" $ares_num [1] 0 $libidn [1] "" > options(width = 120) > devtools::session_info() Session info ----------------------------------------------------------------------------------------------------------- setting value version R Under development (unstable) (2016-10-26 r71594) system x86_64, darwin13.4.0 ui AQUA language (EN) collate en_US.UTF-8 tz America/New_York date 2017-03-01 Packages --------------------------------------------------------------------------------------------------------------- package * version date source bitops * 1.0-6 2013-08-17 CRAN (R 3.4.0) devtools 1.12.0 2016-12-05 CRAN (R 3.4.0) digest 0.6.12 2017-01-27 CRAN (R 3.4.0) memoise 1.0.0 2016-01-29 CRAN (R 3.4.0) RCurl * 1.95-4.8 2016-03-01 CRAN (R 3.4.0) withr 1.0.2 2016-06-20 CRAN (R 3.4.0) And now in R 3.3.2: > library(RCurl) Loading required package: bitops > curlVersion() $age [1] 3 $version [1] "7.51.0" $vesion_num [1] 471808 $host [1] "x86_64-apple-darwin16.0" $features ipv6 ssl libz ntlm asynchdns spnego largefile ntlm_wb 1 4 8 16 128 256 512 32768 $ssl_version [1] "SecureTransport" $ssl_version_num [1] 0 $libz_version [1] "1.2.8" $protocols [1] "dict" "file" "ftp" "ftps" "gopher" "http" "https" "imap" [9] "imaps" "ldap" "ldaps" "pop3" "pop3s" "rtsp" "smb" "smbs" [17] "smtp" "smtps" "telnet" "tftp" $ares [1] "" $ares_num [1] 0 $libidn [1] "" > options(width = 120) > devtools::session_info() Session info ----------------------------------------------------------------------------------------------------------- setting value version R version 3.3.2 RC (2016-10-26 r71594) system x86_64, darwin13.4.0 ui X11 language (EN) collate en_US.UTF-8 tz America/New_York date 2017-03-01 Packages --------------------------------------------------------------------------------------------------------------- package * version date source bitops * 1.0-6 2013-08-17 cran (@1.0-6) colorout * 1.1-2 2016-10-19 Github (jalvesaq/colorout@6d84420) devtools 1.12.0 2016-06-24 CRAN (R 3.3.0) digest 0.6.12 2017-01-27 CRAN (R 3.3.2) memoise 1.0.0 2016-01-29 CRAN (R 3.3.0) RCurl * 1.95-4.8 2016-03-01 cran (@1.95-4.) withr 1.0.2 2016-06-20 CRAN (R 3.3.0) _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
