Question: unable to install TCGAbiolinks
0
gravatar for hoseyni.sb
4 months ago by
hoseyni.sb0
hoseyni.sb0 wrote:

hello. i use R 3.6.1 mint 19.1 i try install TCGAbioliks with

BiocManager::install("TCGAbiolinks")

but i get this:(but i delete many lines)

Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05) Installing package(s) 'TCGAbiolinks' also installing the dependencies ‘mvtnorm’, ‘GenomicAlignments’, ‘Rhtslib’, ‘maxstat’, ‘cmprsk’, ‘ShortRead’, ‘DESeq’, ‘Rsamtools’, ‘rtracklayer’, ‘survminer’, ‘EDASeq’, ‘edgeR’, ‘genefilter’, ‘GenomicFeatures’, ‘sva’

trying URL 'https://cloud.r-project.org/src/contrib/mvtnorm_1.0-11.tar.gz' Content type 'application/x-gzip' length 160498 bytes (156 KB)

downloaded 156 KB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/GenomicAlignments_1.20.1.tar.gz' Content type 'application/x-gzip' length 2314963 bytes (2.2 MB)

downloaded 2.2 MB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/Rhtslib_1.16.1.tar.gz' Content type 'application/x-gzip' length 1470655 bytes (1.4 MB)

downloaded 1.4 MB

trying URL 'https://cloud.r-project.org/src/contrib/maxstat_0.7-25.tar.gz' Content type 'application/x-gzip' length 110733 bytes (108 KB)

downloaded 108 KB

trying URL 'https://cloud.r-project.org/src/contrib/cmprsk_2.2-8.tar.gz' Content type 'application/x-gzip' length 45528 bytes (44 KB)

downloaded 44 KB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/ShortRead_1.42.0.tar.gz' Content type 'application/x-gzip' length 5183736 bytes (4.9 MB)

downloaded 4.9 MB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/DESeq_1.36.0.tar.gz' Content type 'application/x-gzip' length 1692053 bytes (1.6 MB)

downloaded 1.6 MB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/Rsamtools_2.0.0.tar.gz' Content type 'application/x-gzip' length 3032214 bytes (2.9 MB)

downloaded 2.9 MB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/rtracklayer_1.44.0.tar.gz' Content type 'application/x-gzip' length 1540317 bytes (1.5 MB)

downloaded 1.5 MB

trying URL 'https://cloud.r-project.org/src/contrib/survminer_0.4.4.tar.gz' Content type 'application/x-gzip' length 3349031 bytes (3.2 MB)

downloaded 3.2 MB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/EDASeq_2.18.0.tar.gz' Content type 'application/x-gzip' length 1021380 bytes (997 KB)

downloaded 997 KB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/edgeR_3.26.5.tar.gz' Content type 'application/x-gzip' length 1475663 bytes (1.4 MB)

downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/genefilter_1.66.0.tar.gz' Content type 'application/x-gzip' length 1419350 bytes (1.4 MB)

downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/GenomicFeatures_1.36.4.tar.gz' Content type 'application/x-gzip' length 1373749 bytes (1.3 MB)

downloaded 1.3 MB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/sva_3.32.1.tar.gz' Content type 'application/x-gzip' length 429465 bytes (419 KB)

downloaded 419 KB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/TCGAbiolinks_2.12.3.tar.gz' Content type 'application/x-gzip' length 56532350 bytes (53.9 MB)

downloaded 53.9 MB

  • installing source package ‘mvtnorm’ ... * package ‘mvtnorm’ successfully unpacked and MD5 sums checked * using staged installation ** libs

gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-p1m1mT/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -DFORTIFYSOURCE=2 -g -c miwa.c -o miwa.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-p1m1mT/r-base-3.6.1=. -fstack-protector-strong -c mvt.f -o mvt.o /bin/bash: gfortran: command not found /usr/lib/R/etc/Makeconf:190: recipe for target 'mvt.o' failed make: * [mvt.o] Error 127 ERROR: compilation failed for package ‘mvtnorm’ * removing ‘/home/behnaz/R/x8664-pc-linux-gnu-library/3.6/mvtnorm’ * installing *source* package ‘Rhtslib’ ... ** using non-staged installation via StagedInstall field ** libs cd "htslib-1.7" && make -f "/usr/lib/R/etc/Makeconf" -f "Makefile.Rhtslib" make[1]: Entering directory '/tmp/RtmpC8LWIp/R.INSTALL17395619c762/Rhtslib/src/htslib-1.7' Makefile.Rhtslib:130: warning: overriding recipe for target '.c.o' /usr/lib/R/etc/Makeconf:167: warning: ignoring old recipe for target '.c.o' gcc -std=gnu99 -g -Wall -O2 -fpic -I. -c -o kfunc.o kfunc.c g. . . cram/cramio.c:57:10: fatal error: bzlib.h: No such file or directory #include <bzlib.h> ^~~~~~~~~ compilation terminated. Makefile.Rhtslib:130: recipe for target 'cram/cramio.o' failed make[1]: Leaving directory '/tmp/RtmpC8LWIp/R.INSTALL17395619c762/Rhtslib/src/htslib-1.7' make[1]: * [cram/cramio.o] Error 1 Makevars.common:23: recipe for target 'htslib' failed make: * [htslib] Error 2 ERROR: compilation failed for package ‘Rhtslib’ * removing ‘/home/behnaz/R/x8664-pc-linux-gnu-library/3.6/Rhtslib’ * installing *source* package ‘cmprsk’ ... ** package ‘cmprsk’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-p1m1mT/r-base-3.6.1=. -fstack-protector-strong -c cincsub.f -o cincsub.o /bin/bash: gfortran: command not found /usr/lib/R/etc/Makeconf:190: recipe for target 'cincsub.o' failed make: * [cincsub.o] Error 127 ERROR: compilation failed for package ‘cmprsk’ * removing ‘/home/behnaz/R/x8664-pc-linux-gnu-library/3.6/cmprsk’ * installing source package ‘edgeR’ ... * using staged installation * libs . . . /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 /usr/share/R/share/make/shlib.mk:6: recipe for target 'edgeR.so' failed make: * [edgeR.so] Error 1 ERROR: compilation failed for package ‘edgeR’ * removing ‘/home/behnaz/R/x86_64-pc-linux-gnu-library/3.6/edgeR’ * installing source package ‘genefilter’ ... * using staged installation * libs . . .

/bin/bash: gfortran: command not found /usr/lib/R/etc/Makeconf:190: recipe for target 'ttest.o' failed make: * [ttest.o] Error 127 ERROR: compilation failed for package ‘genefilter’ * removing ‘/home/behnaz/R/x8664-pc-linux-gnu-library/3.6/genefilter’ ERROR: dependency ‘mvtnorm’ is not available for package ‘maxstat’ * removing ‘/home/behnaz/R/x8664-pc-linux-gnu-library/3.6/maxstat’ ERROR: dependency ‘genefilter’ is not available for package ‘DESeq’ * removing ‘/home/behnaz/R/x8664-pc-linux-gnu-library/3.6/DESeq’ ERROR: dependency ‘Rhtslib’ is not available for package ‘Rsamtools’ * removing ‘/home/behnaz/R/x8664-pc-linux-gnu-library/3.6/Rsamtools’ ERROR: dependency ‘genefilter’ is not available for package ‘sva’ * removing ‘/home/behnaz/R/x8664-pc-linux-gnu-library/3.6/sva’ ERROR: dependency ‘Rsamtools’ is not available for package ‘GenomicAlignments’ * removing ‘/home/behnaz/R/x8664-pc-linux-gnu-library/3.6/GenomicAlignments’ ERROR: dependencies ‘maxstat’, ‘cmprsk’ are not available for package ‘survminer’ * removing ‘/home/behnaz/R/x8664-pc-linux-gnu-library/3.6/survminer’ ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘ShortRead’ * removing ‘/home/behnaz/R/x8664-pc-linux-gnu-library/3.6/ShortRead’ ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’ * removing ‘/home/behnaz/R/x8664-pc-linux-gnu-library/3.6/rtracklayer’ ERROR: dependency ‘rtracklayer’ is not available for package ‘GenomicFeatures’ * removing ‘/home/behnaz/R/x8664-pc-linux-gnu-library/3.6/GenomicFeatures’ ERROR: dependencies ‘ShortRead’, ‘DESeq’, ‘Rsamtools’, ‘GenomicFeatures’ are not available for package ‘EDASeq’ * removing ‘/home/behnaz/R/x8664-pc-linux-gnu-library/3.6/EDASeq’ ERROR: dependencies ‘survminer’, ‘EDASeq’, ‘edgeR’, ‘genefilter’, ‘GenomicFeatures’, ‘sva’ are not available for package ‘TCGAbiolinks’ * removing ‘/home/behnaz/R/x8664-pc-linux-gnu-library/3.6/TCGAbiolinks’

The downloaded source packages are in ‘/tmp/RtmpNPBxAD/downloadedpackages’ Update old packages: 'rJava', 'KernSmooth', 'Matrix', 'mgcv' Update all/some/none? [a/s/n]: a trying URL 'https://cloud.r-project.org/src/contrib/rJava0.9-11.tar.gz' Content type 'application/x-gzip' length 675188 bytes (659 KB)

downloaded 659 KB

  • installing source package ‘rJava’ ... * package ‘rJava’ successfully unpacked and MD5 sums checked * using staged installation checking for gcc... gcc -std=gnu99 . . . checking Java support in R... present: interpreter : '/usr/lib/jvm/default-java/bin/java' archiver : '' compiler : '' header prep.: '' cpp flags : '' java libs : '' configure: error: Java Development Kit (JDK) is missing or not registered in R Make sure R is configured with full Java support (including JDK). Run R CMD javareconf as root to add Java support to R.

If you don't have root privileges, run R CMD javareconf -e to set all Java-related variables and then install rJava.

ERROR: configuration failed for package ‘rJava’ * removing ‘/usr/lib/R/site-library/rJava’ * restoring previous ‘/usr/lib/R/site-library/rJava’

The downloaded source packages are in ‘/tmp/RtmpNPBxAD/downloadedpackages’ trying URL 'https://cloud.r-project.org/src/contrib/KernSmooth2.23-15.tar.gz' Content type 'application/x-gzip' length 24572 bytes (23 KB)

downloaded 23 KB

trying URL 'https://cloud.r-project.org/src/contrib/Matrix_1.2-17.tar.gz' Content type 'application/x-gzip' length 1860456 bytes (1.8 MB)

downloaded 1.8 MB

trying URL 'https://cloud.r-project.org/src/contrib/mgcv_1.8-28.tar.gz' Content type 'application/x-gzip' length 915991 bytes (894 KB)

downloaded 894 KB

  • installing source package ‘KernSmooth’ ... * package ‘KernSmooth’ successfully unpacked and MD5 sums checked * using staged installation * libs gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-p1m1mT/r-base-3.6.1=. -fstack-protector-strong -c blkest.f -o blkest.o /bin/bash: gfortran: command not found /usr/lib/R/etc/Makeconf:190: recipe for target 'blkest.o' failed make: ** [blkest.o] Error 127 ERROR: compilation failed for package ‘KernSmooth’
  • removing ‘/usr/lib/R/library/KernSmooth’
  • restoring previous ‘/usr/lib/R/library/KernSmooth’
  • installing source package ‘Matrix’ ... * package ‘Matrix’ successfully unpacked and MD5 sums checked * using staged installation * libs . . . /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 /usr/share/R/share/make/shlib.mk:6: recipe for target 'Matrix.so' failed make: ** [Matrix.so] Error 1 ERROR: compilation failed for package ‘Matrix’
  • removing ‘/usr/lib/R/library/Matrix’
  • restoring previous ‘/usr/lib/R/library/Matrix’
  • installing source package ‘mgcv’ ... * package ‘mgcv’ successfully unpacked and MD5 sums checked * using staged installation ** libs

/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 /usr/share/R/share/make/shlib.mk:6: recipe for target 'mgcv.so' failed make: * [mgcv.so] Error 1 ERROR: compilation failed for package ‘mgcv’ * removing ‘/usr/lib/R/library/mgcv’ * restoring previous ‘/usr/lib/R/library/mgcv’

The downloaded source packages are in ‘/tmp/RtmpNPBxAD/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done There were 20 warnings (use warnings() to see them)

then i check warnings and get:

1: In install.packages(pkgs = doing, lib = lib, repos = repos, ... : installation of package ‘mvtnorm’ had non-zero exit status 2: In install.packages(pkgs = doing, lib = lib, repos = repos, ... : installation of package ‘Rhtslib’ had non-zero exit status 3: In install.packages(pkgs = doing, lib = lib, repos = repos, ... : installation of package ‘cmprsk’ had non-zero exit status 4: In install.packages(pkgs = doing, lib = lib, repos = repos, ... : installation of package ‘edgeR’ had non-zero exit status 5: In install.packages(pkgs = doing, lib = lib, repos = repos, ... : installation of package ‘genefilter’ had non-zero exit status 6: In install.packages(pkgs = doing, lib = lib, repos = repos, ... : installation of package ‘maxstat’ had non-zero exit status 7: In install.packages(pkgs = doing, lib = lib, repos = repos, ... : installation of package ‘DESeq’ had non-zero exit status 8: In install.packages(pkgs = doing, lib = lib, repos = repos, ... : installation of package ‘Rsamtools’ had non-zero exit status 9: In install.packages(pkgs = doing, lib = lib, repos = repos, ... : installation of package ‘sva’ had non-zero exit status 10: In install.packages(pkgs = doing, lib = lib, repos = repos, ... : installation of package ‘GenomicAlignments’ had non-zero exit status 11: In install.packages(pkgs = doing, lib = lib, repos = repos, ... : installation of package ‘survminer’ had non-zero exit status 12: In install.packages(pkgs = doing, lib = lib, repos = repos, ... : installation of package ‘ShortRead’ had non-zero exit status 13: In install.packages(pkgs = doing, lib = lib, repos = repos, ... : installation of package ‘rtracklayer’ had non-zero exit status 14: In install.packages(pkgs = doing, lib = lib, repos = repos, ... : installation of package ‘GenomicFeatures’ had non-zero exit status 15: In install.packages(pkgs = doing, lib = lib, repos = repos, ... : installation of package ‘EDASeq’ had non-zero exit status 16: In install.packages(pkgs = doing, lib = lib, repos = repos, ... : installation of package ‘TCGAbiolinks’ had non-zero exit status 17: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘rJava’ had non-zero exit status 18: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘KernSmooth’ had non-zero exit status 19: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘Matrix’ had non-zero exit status 20: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘mgcv’ had non-zero exit status

i prevent permission error with check path of installing and use this code: sudo chmod 777 path

please help me!!!!!!!!!

software error • 328 views
ADD COMMENTlink written 4 months ago by hoseyni.sb0

Please take a second to format your post following the instructions at https://support.bioconductor.org/p/117436/ especially surrounding code chunks with triple back-ticks ` ` `

ADD REPLYlink written 4 months ago by Martin Morgan ♦♦ 24k
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