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claraqin / neonMicrobe

Processing NEON soil microbe marker gene sequence data into ASV tables.
GNU Lesser General Public License v3.0
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Install Rhtslib error #44

Closed KaiZhuPhD closed 3 years ago

KaiZhuPhD commented 3 years ago

On Socs-Stats Server, devtools::install_github("claraqin/neonMicrobe") hits a roadblock when installing the Rhtslib package. I followed the instruction on https://bioconductor.org/packages/release/bioc/html/Rhtslib.html, but here're the error messages. R v 3.6 has similar messages.

> BiocManager::install("Rhtslib", type = "source")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installing package(s) 'Rhtslib'
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 1437k  100 1437k    0     0  16.5M      0 --:--:-- --:--:-- --:--:-- 16.5M
Microsoft R Open 4.0.2
The enhanced R distribution from Microsoft
Microsoft packages Copyright (C) 2020 Microsoft Corporation

Using the Intel MKL for parallel mathematical computing (using 44 cores).

Default CRAN mirror snapshot taken on 2020-07-16.
See: https://mran.microsoft.com/.

* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.7" && make -f "/opt/microsoft/ropen/4.0.2/lib64/R/etc/Makeconf" -f "Makefile.Rhtslib"
make[1]: Entering directory '/tmp/Rtmptxl4sR/R.INSTALLecb550d6d643/Rhtslib/src/htslib-1.7'
Makefile.Rhtslib:128: warning: overriding recipe for target '.c.o'
/opt/microsoft/ropen/4.0.2/lib64/R/etc/Makeconf:159: warning: ignoring old recipe for target '.c.o'
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c
gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -I. -DU_STATIC_IMPLEMENTATION -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c
cram/cram_io.c:61:18: fatal error: lzma.h: No such file or directory
compilation terminated.
make[1]: *** [Makefile.Rhtslib:128: cram/cram_io.o] Error 1
make[1]: Leaving directory '/tmp/Rtmptxl4sR/R.INSTALLecb550d6d643/Rhtslib/src/htslib-1.7'
make: *** [Makevars.common:24: htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/raid/users/kai.zhu/R/x86_64-pc-linux-gnu-library/4.0/Rhtslib’

The downloaded source packages are in
    ‘/tmp/RtmppVM9FP/downloaded_packages’
Installation path not writeable, unable to update packages: BiocGenerics,
  BiocManager, broom, callr, cli, cpp11, data.table, dbplyr, DelayedArray, desc,
  devtools, diffobj, dplyr, DT, e1071, farver, formatR, GenomeInfoDb, gert, gh,
  haven, highr, IRanges, isoband, knitr, lubridate, lwgeom, magick,
  MatrixGenerics, mgcv, neonUtilities, nngeo, packrat, parallelly, pillar,
  pkgload, processx, ps, RcppArmadillo, RcppParallel, RCurl, remotes, reprex,
  reticulate, rmarkdown, rsconnect, rvest, S4Vectors, sf, spatstat,
  spatstat.data, spatstat.geom, spatstat.sparse, spatstat.utils, surveillance,
  survival, tensorflow, tfruns, tibble, tidyr, tidyverse, tinytex, units, utf8,
  vctrs, viridisLite, waldo, withr, wk, xfun, zoo
Warning message:
In install.packages(...) :
  installation of package ‘Rhtslib’ had non-zero exit status
rbartelme commented 3 years ago

@KaiZhuPhD I think this is because it can't find the lzma.h see the lines:

cram/cram_io.c:61:18: fatal error: lzma.h: No such file or directory
compilation terminated.
make[1]: *** [Makefile.Rhtslib:128: cram/cram_io.o] Error 1
make[1]: Leaving directory '/tmp/Rtmptxl4sR/R.INSTALLecb550d6d643/Rhtslib/src/htslib-1.7'
make: *** [Makevars.common:24: htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/raid/users/kai.zhu/R/x86_64-pc-linux-gnu-library/4.0/Rhtslib’

I think this is error is due to missing the xz utils package on that particular system.

claraqin commented 3 years ago

Since this seems to be an issue on socs-stats's end, I'll close this issue, and ask Doug for help in debugging this on socs-stats.

If this is presenting a barrier to your use, though, you might consider switching to the recently-updated CyVerse App. @rbartelme has just written some documentation on how to use it here: https://github.com/claraqin/neonMicrobe/blob/docker/docker/docker.md