[Bioc-devel] Error with compiling Rhtslib
James W. MacDonald
jm@cdon @end|ng |rom uw@edu
Thu Oct 17 22:20:15 CEST 2019
This isn't a bioc-devel question. This listserv is intended for people with
package development questions, not general problems, which should be asked
on the support site.
And when I Google 'lzma.h' (which you could do as well), one of the answers
is
https://stackoverflow.com/questions/22738077/backports-lzma-lzmamodule-c11518-fatal-error-lzma-h-no-such-file-or-direct,
which indicates you need to do
brew install xz
if you are using homebrew.
On Thu, Oct 17, 2019 at 4:11 PM Yuelin Zhu <yuelin using gmail.com> wrote:
> Hi,
>
> It looks like Rhtslib can not be compiled for R_devel and the main error
> message says: cram/cram_io.c:61:10: fatal error: 'lzma.h' file not found
>
> Please see details below:
>
> > BiocManager::install("Rhtslib")
> Bioconductor version 3.10 (BiocManager 1.30.8), R Under development
> (unstable)
> (2019-10-17 r77304)
> Installing package(s) 'Rhtslib'
> Warning: unable to access index for repository
>
> https://bioconductor.org/packages/3.10/bioc/bin/macosx/el-capitan/contrib/4.0
> :
> cannot open URL '
>
> https://bioconductor.org/packages/3.10/bioc/bin/macosx/el-capitan/contrib/4.0/PACKAGES
> '
> Warning: unable to access index for repository
>
> https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/4.0
> :
> cannot open URL '
>
> https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/4.0/PACKAGES
> '
> Warning: unable to access index for repository
>
> https://bioconductor.org/packages/3.10/data/experiment/bin/macosx/el-capitan/contrib/4.0
> :
> cannot open URL '
>
> https://bioconductor.org/packages/3.10/data/experiment/bin/macosx/el-capitan/contrib/4.0/PACKAGES
> '
> Warning: unable to access index for repository
>
> https://bioconductor.org/packages/3.10/workflows/bin/macosx/el-capitan/contrib/4.0
> :
> cannot open URL '
>
> https://bioconductor.org/packages/3.10/workflows/bin/macosx/el-capitan/contrib/4.0/PACKAGES
> '
> Warning: unable to access index for repository
> https://cran.rstudio.com/bin/macosx/el-capitan/contrib/4.0:
> cannot open URL '
> https://cran.rstudio.com/bin/macosx/el-capitan/contrib/4.0/PACKAGES'
> Package which is only available in source form, and may need
> compilation of C/C++/Fortran: 'Rhtslib'
> Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
> installing the source package 'Rhtslib'
>
> trying URL '
>
> https://bioconductor.org/packages/3.10/bioc/src/contrib/Rhtslib_1.17.9.tar.gz
> '
> Content type 'application/x-gzip' length 1471032 bytes (1.4 MB)
> ==================================================
> downloaded 1.4 MB
>
> * installing *source* package ‘Rhtslib’ ...
> ** using non-staged installation via StagedInstall field
> ** libs
> cd "htslib-1.7" && make -f
> "/Library/Frameworks/R.framework/Resources/etc/Makeconf" -f
> "Makefile.Rhtslib"
> Makefile.Rhtslib:128: warning: overriding commands for target `.c.o'
> /Library/Frameworks/R.framework/Resources/etc/Makeconf:166: warning:
> ignoring old commands for target `.c.o'
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c
> echo '#define HTS_VERSION "1.7"' > version.h
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c
> clang -Wall -g -O2 -fpic -I. -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include
> -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c
>
> *cram/cram_io.c:61:10: fatal error: 'lzma.h' file not found*#include
> <lzma.h>
> ^~~~~~~~
> 1 error generated.
> make[1]: *** [cram/cram_io.o] Error 1
> make: *** [htslib] Error 2
> ERROR: compilation failed for package ‘Rhtslib’
> * removing
> ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib’
> * restoring previous
> ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib’
>
> The downloaded source packages are in
>
> '/private/var/folders/c0/dsy4zf0d75x8wp0w89r8g89nh1q7rl/T/RtmpKdZbDO/downloaded_packages'
> Warning message:
> In install.packages(...) :
> installation of package 'Rhtslib' had non-zero exit status
>
> > sessionInfo()
> R Under development (unstable) (2019-10-17 r77304)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Mojave 10.14.6
>
> Matrix products: default
> BLAS:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.0.dylib
> LAPACK:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
>
> 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] stats4 parallel stats graphics grDevices utils datasets
> [8] methods base
>
> other attached packages:
> [1] scran_1.13.30 scater_1.13.25
> [3] ggplot2_3.2.1 ensembldb_2.9.6
> [5] AnnotationFilter_1.9.0 GenomicFeatures_1.37.4
> [7] AnnotationDbi_1.47.1 AnnotationHub_2.17.10
> [9] BiocFileCache_1.9.1 dbplyr_1.4.2
> [11] Rtsne_0.15 DropletUtils_1.5.10
> [13] SingleCellExperiment_1.7.11 SummarizedExperiment_1.15.9
> [15] DelayedArray_0.11.8 BiocParallel_1.19.3
> [17] matrixStats_0.55.0 Biobase_2.45.1
> [19] Rhdf5lib_1.7.6 Rhtslib_1.17.9
> [21] Rsamtools_2.1.7 Biostrings_2.53.2
> [23] XVector_0.25.0 GenomicRanges_1.37.17
> [25] GenomeInfoDb_1.21.2 IRanges_2.19.17
> [27] S4Vectors_0.23.25 BiocGenerics_0.31.6
>
> loaded via a namespace (and not attached):
> [1] ggbeeswarm_0.6.0 colorspace_1.4-1
> [3] BiocNeighbors_1.3.5 bit64_0.9-7
> [5] interactiveDisplayBase_1.23.0 RSpectra_0.15-0
> [7] R.methodsS3_1.7.1 zeallot_0.1.0
> [9] R.oo_1.22.0 uwot_0.1.4
> [11] shiny_1.4.0 HDF5Array_1.13.10
> [13] BiocManager_1.30.8 compiler_4.0.0
> [15] httr_1.4.1 dqrng_0.2.1
> [17] backports_1.1.5 assertthat_0.2.1
> [19] Matrix_1.2-17 fastmap_1.0.1
> [21] lazyeval_0.2.2 limma_3.41.18
> [23] later_1.0.0 BiocSingular_1.1.7
> [25] htmltools_0.4.0 prettyunits_1.0.2
> [27] tools_4.0.0 rsvd_1.0.2
> [29] igraph_1.2.4.1 gtable_0.3.0
> [31] glue_1.3.1 GenomeInfoDbData_1.2.1
> [33] dplyr_0.8.3 rappdirs_0.3.1
> [35] Rcpp_1.0.2 vctrs_0.2.0
> [37] rtracklayer_1.45.6 DelayedMatrixStats_1.7.2
> [39] stringr_1.4.0 mime_0.7
> [41] irlba_2.3.3 statmod_1.4.32
> [43] XML_3.98-1.20 edgeR_3.27.13
> [45] zlibbioc_1.31.0 scales_1.0.0
> [47] hms_0.5.1 promises_1.1.0
> [49] ProtGenerics_1.17.4 rhdf5_2.29.5
> [51] yaml_2.2.0 curl_4.2
> [53] memoise_1.1.0 gridExtra_2.3
> [55] biomaRt_2.41.9 stringi_1.4.3
> [57] RSQLite_2.1.2 rlang_0.4.0
> [59] pkgconfig_2.0.3 bitops_1.0-6
> [61] lattice_0.20-38 purrr_0.3.2
> [63] GenomicAlignments_1.21.7 labeling_0.3
> [65] cowplot_1.0.0 bit_1.1-14
> [67] tidyselect_0.2.5 magrittr_1.5
> [69] R6_2.4.0 DBI_1.0.0
> [71] pillar_1.4.2 withr_2.1.2
> [73] RCurl_1.95-4.12 tibble_2.1.3
> [75] crayon_1.3.4 viridis_0.5.1
> [77] progress_1.2.2 locfit_1.5-9.1
> [79] grid_4.0.0 blob_1.2.0
> [81] FNN_1.1.3 digest_0.6.21
> [83] xtable_1.8-4 httpuv_1.5.2
> [85] R.utils_2.9.0 openssl_1.4.1
> [87] RcppParallel_4.4.4 munsell_0.5.0
> [89] beeswarm_0.2.3 viridisLite_0.3.0
> [91] vipor_0.4.5 tcltk_4.0.0
> [93] askpass_1.1
>
> Thanks,
>
> Jack
> ----
> Yuelin Jack Zhu
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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