You're using R-devel, whereas Bioconductor is using R-3.6.x for both our
release and devel branches. Consequently, you're being required to compile from
source, rather than using the pre-built binaries. For this reason, your system
needs to have the necessary libraries and their headers; this will not be
required once Bioconductor's devel branch starts to use R-devel in a couple of
weeks; the pre-built binaries will not require you to have any additional
software.
Personally, I suggest you continue to use the supported versions of R and
Bioconductor. If you want to use the devel version of R, then arrange to
install liblzma and header files; I think the magic using brew is close to
`brew install xz`.
Martin
On 10/17/19, 4:09 PM, "Bioc-devel on behalf of Yuelin Zhu"
<bioc-devel-boun...@r-project.org on behalf of yue...@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
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