Query regarding error in installation of "microbiomeutilities" R package
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abhisek001 • 0
@6d5973d2
Last seen 7 days ago
India

Hello there, I am trying to install a Bioconductor package from this website (https://microsud.github.io/microbiomeutilities/) but I cannot troubleshoot due to a large number of errors in the installation process. If any expert can help me with kind support it will be highly appreciated. Thanks

The error code is the following. I tried to install the dependency packages eg. ‘microbiome’, ‘ggpubr’ but those packages also not installed.

/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: nloptr.so] Error 1
ERROR: compilation failed for package ‘nloptr’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/nloptr’
* installing *source* package ‘minqa’ ...
** package ‘minqa’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong  -c altmov.f -o altmov.o
/bin/bash: gfortran: command not found
make: *** [/usr/lib/R/etc/Makeconf:192: altmov.o] Error 127
ERROR: compilation failed for package ‘minqa’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/minqa’
ERROR: dependencies ‘minqa’, ‘nloptr’ are not available for package ‘lme4’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/lme4’
ERROR: dependency ‘SparseM’ is not available for package ‘quantreg’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/quantreg’
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/pbkrtest’
ERROR: dependencies ‘pbkrtest’, ‘quantreg’, ‘lme4’ are not available for package ‘car’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/car’
ERROR: dependency ‘car’ is not available for package ‘rstatix’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/rstatix’
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/ggpubr’

The downloaded source packages are in
    ‘/tmp/RtmpGJi8si/downloaded_packages’
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/tmp/RtmpGJi8si/remotes11d44c9c8628/microsud-microbiomeutilities-046a9f9/DESCRIPTION’ ...
─  preparing ‘microbiomeutilities’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘microbiomeutilities_1.00.17.tar.gz’

Installing package into ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
ERROR: dependencies ‘microbiome’, ‘ggpubr’ are not available for package ‘microbiomeutilities’
* removing ‘/home/omic/R/x86_64-pc-linux-gnu-library/4.2/microbiomeutilities’
There were 11 warnings (use warnings() to see them)
MicrobiomeData R microbiomeutilities Install • 934 views
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ATpoint ★ 4.2k
@atpoint-13662
Last seen 1 day ago
Germany

This is not a Bioconductor package so you should find answers at StackOverflow rather than here.

As a general rule for compilation errors: Google the first error that pops up (here that is missing llapack), read the StackOverflow tophit https://stackoverflow.com/questions/27033243/usr-bin-ld-cannot-find-llapack and try again to install the package. Repeat until solved for all error messages. If tast doesn't work out and all googling doesn't help then open a wiestion here for Bioconductor packages or StackOverflow for general software-related questions.

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Thank you so much for guiding me, the issue is resolved now.

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