Problem installing methylKit on Mac

[sr320]

FFS

Why is this so hard?

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.14")

BiocManager::install(c("methylKit"))

error

'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.1 (2021-08-10)
Installing package(s) 'methylKit'
also installing the dependencies ‘GenomicAlignments’, ‘Rsamtools’, ‘rtracklayer’, ‘Rhtslib’

Warning in .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
Warning in .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
Warning in .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
Warning in .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
Warning in .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
Packages which are only available in source form, and may need
  compilation of C/C++/Fortran: ‘GenomicAlignments’ ‘Rsamtools’
  ‘rtracklayer’ ‘Rhtslib’ ‘methylKit’
installing the source packages ‘GenomicAlignments’, ‘Rsamtools’, ‘rtracklayer’, ‘Rhtslib’, ‘methylKit’

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/GenomicAlignments_1.30.0.tar.gz'
Content type 'application/x-gzip' length 2300932 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/Rsamtools_2.10.0.tar.gz'
Content type 'application/x-gzip' length 2870706 bytes (2.7 MB)
==================================================
downloaded 2.7 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/rtracklayer_1.54.0.tar.gz'
Content type 'application/x-gzip' length 4054546 bytes (3.9 MB)
==================================================
downloaded 3.9 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/Rhtslib_1.26.0.tar.gz'
Content type 'application/x-gzip' length 1470165 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/methylKit_1.20.0.tar.gz'
Content type 'application/x-gzip' length 1327901 bytes (1.3 MB)
==================================================
downloaded 1.3 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:168: warning: ignoring old commands for target `.c.o'
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/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/4.1-arm64/Resources/library/Rhtslib’
Warning in .inet_warning(msg) :
  installation of package ‘Rhtslib’ had non-zero exit status
ERROR: dependency ‘Rhtslib’ is not available for package ‘Rsamtools’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rsamtools’
Warning in .inet_warning(msg) :
  installation of package ‘Rsamtools’ had non-zero exit status
ERROR: dependency ‘Rsamtools’ is not available for package ‘GenomicAlignments’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/GenomicAlignments’
Warning in .inet_warning(msg) :
  installation of package ‘GenomicAlignments’ had non-zero exit status
ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/rtracklayer’
Warning in .inet_warning(msg) :
  installation of package ‘rtracklayer’ had non-zero exit status
ERROR: dependencies ‘Rsamtools’, ‘rtracklayer’, ‘Rhtslib’ are not available for package ‘methylKit’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/methylKit’
Warning in .inet_warning(msg) :
  installation of package ‘methylKit’ had non-zero exit status

The downloaded source packages are in
	‘/private/var/folders/cz/yz29q78x4gv89hzvdmgb_9vh0000gn/T/RtmprjW9Bw/downloaded_packages’

[kubu4]

Try again without the vector designation (get rid the c().

[kubu4]

After the last attempt (where you answered "no" to installing from sources), have you tried loading methylKit?

It's possible it installed correctly.

As for those warnings, those are just warnings and don't indicate any sort of failure and, as it turns out, are related to having the M1 chip in your Mac. See this thread:

https://support.bioconductor.org/p/9139482/#9139605

[sr320]

loading library

Error in library(methylKit) : there is no package called ‘methylKit’

[kubu4]

Thanks.

Alrighty, since the problem is this missing header file (lzma.h), you can install the library that it's looking for using homebrew.

Before installing, I'd close R and/or RStudio (and don't save session history). Then, install it:

brew install xz

After that, I'd also close any open Terminal windows before launching R/RStudio - just to make sure the system is fully refreshed.

Now, from my sleuthing, this will install the necessary library, but it's not uncommon for R to fail to find it.

Regardless, it's worth a shot.

[sr320]

Done...
trying install again..

what is the correct answer to

Do you want to attempt to install these from sources? (Yes/no/cancel)

[sr320]

tried no, then yes....

still library not loading...

[kubu4]

From this thread:

Please be aware that Bioconductor does not support the Apple M1 (a.k.a. arm64) architecture in native mode yet, only via Rosetta, which is the emulator built into macOS Big Sur that enables Mac M1 systems to run Intel x86_64 apps. Concretely this means that if you are on an Apple M1 system, we strongly recommend that you use the official Intel 64-bit R (x86_64 arch) from CRAN available here: https://cran.r-project.org/bin/macosx/ (choose R-4.1.0.pkg, NOT R-4.1.0-arm64.pkg). This will run on the Apple M1 platform in emulation mode.

So, it looks like you need to download and install the Intel version of R.

[sr320]

That was it!
Just install the version of R meant for a different machine 🥲

[kubu4]

FFS

Why is this so hard?

BTW, I didn't want to react with a laughing emoji at the time, because I could fully appreciate the frustration, but this did make me laugh. It's insane how much frustration I consistently encounter when dealing with installing R stuff; especially BioConductor. I feel like that thought goes through my head every time.