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goseq installation issues

Light1992
Sep 20th, 2019
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  1. [root@localhost Lattuga]# R
  2.  
  3. R version 3.5.3 (2019-03-11) -- "Great Truth"
  4. Copyright (C) 2019 The R Foundation for Statistical Computing
  5. Platform: x86_64-pc-linux-gnu (64-bit)
  6.  
  7. R è un software libero ed è rilasciato SENZA ALCUNA GARANZIA.
  8. Siamo ben lieti se potrai redistribuirlo, ma sotto certe condizioni.
  9. Scrivi 'license()' o 'licence()' per dettagli su come distribuirlo.
  10.  
  11. R è un progetto di collaborazione con molti contributi esterni.
  12. Scrivi 'contributors()' per maggiori informazioni e 'citation()'
  13. per sapere come citare R o i pacchetti di R nelle pubblicazioni.
  14.  
  15. Scrivi 'demo()' per una dimostrazione, 'help()' per la guida in linea, o
  16. 'help.start()' per l'help navigabile con browser HTML.
  17. Scrivi 'q()' per uscire da R.
  18.  
  19. [Caricato workspace precedentemente salvato]
  20.  
  21. > if (!requireNamespace("BiocManager", quietly = TRUE))
  22. install.packages("BiocManager")
  23.  
  24. BiocManager::install("goseq")+ > >
  25. Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.3 (2019-03-11)
  26. Installing package(s) 'goseq'
  27. also installing the dependencies ‘curl’, ‘httr’, ‘biomaRt’, ‘GenomicFeatures’, ‘geneLenDataBase’
  28.  
  29. provo con l'URL 'https://cran.rstudio.com/src/contrib/curl_4.1.tar.gz'
  30. Content type 'application/x-gzip' length 667788 bytes (652 KB)
  31. ==================================================
  32. downloaded 652 KB
  33.  
  34. provo con l'URL 'https://cran.rstudio.com/src/contrib/httr_1.4.1.tar.gz'
  35. Content type 'application/x-gzip' length 158465 bytes (154 KB)
  36. ==================================================
  37. downloaded 154 KB
  38.  
  39. provo con l'URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/biomaRt_2.38.0.tar.gz'
  40. Content type 'application/x-gzip' length 291202 bytes (284 KB)
  41. ==================================================
  42. downloaded 284 KB
  43.  
  44. provo con l'URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/GenomicFeatures_1.34.8.tar.gz'
  45. Content type 'application/x-gzip' length 1370941 bytes (1.3 MB)
  46. ==================================================
  47. downloaded 1.3 MB
  48.  
  49. provo con l'URL 'https://bioconductor.org/packages/3.8/data/experiment/src/contrib/geneLenDataBase_1.18.0.tar.gz'
  50. Content type 'application/x-gzip' length 100436341 bytes (95.8 MB)
  51. ==================================================
  52. downloaded 95.8 MB
  53.  
  54. provo con l'URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/goseq_1.34.1.tar.gz'
  55. Content type 'application/x-gzip' length 783446 bytes (765 KB)
  56. ==================================================
  57. downloaded 765 KB
  58.  
  59. * installing *source* package ‘curl’ ...
  60. ** package ‘curl’ successfully unpacked and MD5 sums checked
  61. Found pkg-config cflags and libs!
  62. Using PKG_CFLAGS=
  63. Using PKG_LIBS=-lcurl
  64. ** libs
  65. rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o
  66. gcc -std=gnu99 -I"/usr/local/lib64/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c callbacks.c -o callbacks.o
  67. gcc -std=gnu99 -I"/usr/local/lib64/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c curl.c -o curl.o
  68. gcc -std=gnu99 -I"/usr/local/lib64/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c download.c -o download.o
  69. gcc -std=gnu99 -I"/usr/local/lib64/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c escape.c -o escape.o
  70. gcc -std=gnu99 -I"/usr/local/lib64/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c fetch.c -o fetch.o
  71. gcc -std=gnu99 -I"/usr/local/lib64/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c form.c -o form.o
  72. gcc -std=gnu99 -I"/usr/local/lib64/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c getdate.c -o getdate.o
  73. gcc -std=gnu99 -I"/usr/local/lib64/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c handle.c -o handle.o
  74. handle.c:30:1: error: unknown type name ‘curl_sslbackend’
  75. curl_sslbackend default_ssl_backend;
  76. ^
  77. make: *** [handle.o] Errore 1
  78. ERROR: compilation failed for package ‘curl’
  79. * removing ‘/usr/local/lib64/R/library/curl’
  80. ERROR: dependency ‘curl’ is not available for package ‘httr’
  81. * removing ‘/usr/local/lib64/R/library/httr’
  82. ERROR: dependency ‘httr’ is not available for package ‘biomaRt’
  83. * removing ‘/usr/local/lib64/R/library/biomaRt’
  84. ERROR: dependency ‘biomaRt’ is not available for package ‘GenomicFeatures’
  85. * removing ‘/usr/local/lib64/R/library/GenomicFeatures’
  86. ERROR: dependency ‘GenomicFeatures’ is not available for package ‘geneLenDataBase’
  87. * removing ‘/usr/local/lib64/R/library/geneLenDataBase’
  88. ERROR: dependency ‘geneLenDataBase’ is not available for package ‘goseq’
  89. * removing ‘/usr/local/lib64/R/library/goseq’
  90.  
  91. The downloaded source packages are in
  92. ‘/tmp/Rtmp1BgAoA/downloaded_packages’
  93. Updating HTML index of packages in '.Library'
  94. Making 'packages.html' ... done
  95. Warning messages:
  96. 1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  97. installation of package ‘curl’ had non-zero exit status
  98. 2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  99. installation of package ‘httr’ had non-zero exit status
  100. 3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  101. installation of package ‘biomaRt’ had non-zero exit status
  102. 4: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  103. installation of package ‘GenomicFeatures’ had non-zero exit status
  104. 5: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  105. installation of package ‘geneLenDataBase’ had non-zero exit status
  106. 6: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  107. installation of package ‘goseq’ had non-zero exit status
  108. > sessionInfo()
  109. R version 3.5.3 (2019-03-11)
  110. Platform: x86_64-pc-linux-gnu (64-bit)
  111. Running under: CentOS Linux 7 (Core)
  112.  
  113. Matrix products: default
  114. BLAS: /usr/local/lib64/R/lib/libRblas.so
  115. LAPACK: /usr/local/lib64/R/lib/libRlapack.so
  116.  
  117. locale:
  118. [1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C
  119. [3] LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8
  120. [5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=it_IT.UTF-8
  121. [7] LC_PAPER=it_IT.UTF-8 LC_NAME=C
  122. [9] LC_ADDRESS=C LC_TELEPHONE=C
  123. [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
  124.  
  125. attached base packages:
  126. [1] stats graphics grDevices utils datasets methods base
  127.  
  128. loaded via a namespace (and not attached):
  129. [1] BiocManager_1.30.4 compiler_3.5.3 tools_3.5.3
  130. >
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