lmolla commented 6 years ago

I am running into problems with installing this package in R I am not sure why this is happening.

install.packages("openssl")

There is a binary version available but the source version is later: binary source needs_compilation openssl 0.9.6 0.9.7 TRUE

Do you want to install from sources the package which needs compilation? y/n: y installing the source package ‘openssl’

openssl_0.9.7.tar.gz' Content type 'unknown' length 1243577 bytes (1.2 MB)

downloaded 1.2 MB

installing source package ‘openssl’ ... ** package ‘openssl’ successfully unpacked and MD5 sums checked 0.9.5 Using PKG_CFLAGS=-I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/openssl/include ------------------------- ANTICONF ERROR --------------------------- Configuration failed because openssl was not found. Try installing:
- deb: libssl-dev (Debian, Ubuntu, etc)
- rpm: openssl-devel (Fedora, CentOS, RHEL)
- csw: libssl_dev (Solaris)
- brew: openssl@1.1 (Mac OSX) If openssl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
  
  ERROR: configuration failed for package ‘openssl’
removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/openssl’
restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/openssl’ Warning in install.packages : installation of package ‘openssl’ had non-zero exit status

The downloaded source packages are in ‘/private/var/folders/ll/zscj8q4j7_xb_dmj_cmt5n580000gp/T/Rtmpx9UQEu/downloaded_packages’

sessionInfo() R version 3.3.3 (2017-03-06) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X Mavericks 10.9.5

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] devtools_1.13.3 BiocInstaller_1.24.0 biomaRt_2.30.0 methylKit_1.0.0 GenomicRanges_1.26.4 [6] GenomeInfoDb_1.10.3 IRanges_2.8.2 S4Vectors_0.12.2 BiocGenerics_0.20.0

loaded via a namespace (and not attached): [1] SummarizedExperiment_1.4.0 qvalue_2.6.0 gtools_3.5.0 reshape2_1.4.2
[5] splines_3.3.3 lattice_0.20-35 colorspace_1.3-2 rtracklayer_1.34.2
[9] blob_1.1.0 XML_3.98-1.9 rlang_0.1.2 R.oo_1.21.0
[13] withr_2.1.0 DBI_0.7 R.utils_2.5.0 BiocParallel_1.8.2
[17] fastseg_1.20.0 bit64_0.9-7 plyr_1.8.4 stringr_1.2.0
[21] zlibbioc_1.20.0 Biostrings_2.42.1 munsell_0.4.3 gtable_0.2.0
[25] R.methodsS3_1.7.1 coda_0.19-1 memoise_1.1.0 knitr_1.17
[29] Biobase_2.34.0 curl_3.0 AnnotationDbi_1.36.2 Rcpp_0.12.13
[33] scales_0.5.0 limma_3.30.13 XVector_0.14.1 bit_1.1-12
[37] Rsamtools_1.26.2 ggplot2_2.2.1 digest_0.6.12 stringi_1.1.5
[41] numDeriv_2016.8-1 grid_3.3.3 tools_3.3.3 bitops_1.0-6
[45] bbmle_1.0.20 magrittr_1.5 lazyeval_0.2.1 RCurl_1.95-4.8
[49] tibble_1.3.4 RSQLite_2.0 MASS_7.3-47 Matrix_1.2-11
[53] data.table_1.10.4-3 httr_1.3.1 emdbook_1.3.9 R6_2.2.2
[57] mclust_5.3 git2r_0.19.0 GenomicAlignments_1.10.1

jeroen commented 6 years ago

Yes I know it's a small bug. For now just answer n on Do you want to install from sources the package which needs compilation?

jeroen commented 6 years ago

New version is on CRAN. Both binary pkg and source pkg should now work.

jeroen / openssl

Unable to install openssl in MAC version 10.9.5 #52

trying URL 'https://cran.rstudio.com/src/contrib/openssl_0.9.7.tar.gz' Content type 'unknown' length 1243577 bytes (1.2 MB)

brew: openssl@1.1 (Mac OSX) If openssl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'