[mcm]

... I may not understand the r-3.x part... Without it, the output is "Operation not permitted".

$ which R
/usr/bin/R
$ ls -l /usr/bin/R
-rwxr-xr-x 1 root root 8589 Oct 25 2013 /usr/bin/R
$ chown -R my_account_name /usr/bin/R
chown: changing ownership of ‘/usr/bin/R’: Operation not permitted
$ chgrp -R my_group /usr/bin/R
chgrp: changing group of ‘/usr/bin/R’: Operation not permitted

[GenoMax]

I was afraid that your R install may be owned by root, which seems to be the case. (/usr/bin/R is probably a shell script).

Can you su to root and then try cummerbund install in R? Some people may not like this method but since you are the only user on the system that is probably ok in your case (changes made as root affect all users on the system).

[mcm]

Dear GenoMax,
I could not su to root (authentication failed). However, I finally got it working... I managed to upgrade R (I had tried before but with no success) to version 3.1.3 and now everything works.
Thank you so, so much for all your suggestions and replying so fast. You were a real support!! Hopefully now I can visualize super good results and then the week will be perfect
Have a great day!!

[mfahim]

After applying most of the solutions mentioned above.. I am still getting this message..

Error : objects ‘metadata’, ‘isTRUEorFALSE’, ‘isSingleString’ are not exported by 'namespace:IRanges'
Error: package ‘Gviz’ could not be loaded

I tried installing Gviz..


rror : object ‘renameSeqlevels’ is not exported by 'namespace:GenomicRanges'
ERROR: lazy loading failed for package ‘Gviz’
* removing ‘/home/fahimish/R/x86_64-pc-linux-gnu-library/3.2/Gviz’
Warning in install.packages :
installation of package ‘/home/fahimish/Downloads/r-bioc-gviz_1.8.4.orig.tar.gz’ had non-zero exit status

need your help.
Thanks in advance

[Chinboy]

How to solve this problem?


> library(cummeRbund)
载入需要的程辑包：BiocGenerics
载入需要的程辑包：parallel

载入程辑包：‘BiocGenerics’

The following objects are masked from ‘packagearallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unlist, unsplit

载入需要的程辑包：RSQLite
载入需要的程辑包：DBI
载入需要的程辑包：ggplot2
载入需要的程辑包：reshape2
载入需要的程辑包：fastcluster

载入程辑包：‘fastcluster’

The following object is masked from ‘package:stats’:

hclust

载入需要的程辑包：rtracklayer
载入需要的程辑包：GenomicRanges
载入需要的程辑包：S4Vectors
载入需要的程辑包：stats4
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
载入需要的程辑包：IRanges
载入需要的程辑包：GenomeInfoDb
载入需要的程辑包：Gviz
载入需要的程辑包：grid

载入程辑包：‘cummeRbund’

The following object is masked from ‘package:GenomicRanges’:

promoters

The following object is masked from ‘package:IRanges’:

promoters

The following object is masked from ‘package:BiocGenerics’:

conditions
thanks a lot

[k.h]

how to install cummeRbund successfuly

Dear all,

I am installing cummeRbund but I am getting the following error;

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
> biocLite("cummeRbund")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘cummeRbund’
also installing the dependencies ‘curl’, ‘openssl’, ‘httr’, ‘AnnotationHub’, ‘VariantAnnotation’, ‘ensembldb’, ‘XML’, ‘RCurl’, ‘biomaRt’, ‘GenomicFeatures’, ‘BSgenome’, ‘biovizBase’, ‘rtracklayer’, ‘Gviz’

trying URL 'https://cran.rstudio.com/src/contrib/curl_0.9.7.tar.gz'
Content type 'unknown' length 263926 bytes (257 KB)
==================================================
downloaded 257 KB

trying URL 'https://cran.rstudio.com/src/contrib/openssl_0.9.4.tar.gz'
Content type 'unknown' length 1165388 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/src/contrib/httr_1.2.1.tar.gz'
Content type 'unknown' length 133398 bytes (130 KB)
==================================================
downloaded 130 KB

trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/AnnotationHub_2.4.2.tar.gz'
Content type 'unknown' length 415393 bytes (405 KB)
==================================================
downloaded 405 KB

trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/VariantAnnotation_1.18.5.tar.gz'
Content type 'unknown' length 1636519 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/ensembldb_1.4.7.tar.gz'
Content type 'unknown' length 1231735 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.4.tar.gz'
Content type 'unknown' length 1599214 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/src/contrib/RCurl_1.95-4.8.tar.gz'
Content type 'unknown' length 916934 bytes (895 KB)
==================================================
downloaded 895 KB

trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/biomaRt_2.28.0.tar.gz'
Content type 'unknown' length 274747 bytes (268 KB)
==================================================
downloaded 268 KB

trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/GenomicFeatures_1.24.4.tar.gz'
Content type 'unknown' length 827977 bytes (808 KB)
==================================================
downloaded 808 KB

trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/BSgenome_1.40.1.tar.gz'
Content type 'unknown' length 6059426 bytes (5.8 MB)
==================================================
downloaded 5.8 MB

trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/biovizBase_1.20.0.tar.gz'
Content type 'unknown' length 2432033 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/rtracklayer_1.32.1.tar.gz'
Content type 'unknown' length 1378505 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/Gviz_1.16.1.tar.gz'
Content type 'unknown' length 3387915 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/cummeRbund_2.14.0.tar.gz'
Content type 'unknown' length 2317146 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
* deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
* rpm: libcurl-devel (Fedora, CentOS, RHEL)
* csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/curl’
* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
Using PKG_CFLAGS=
Using PKG_LIBS=-lssl -lcrypto
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because openssl was not found. Try installing:
* deb: libssl-dev (Debian, Ubuntu, etc)
* rpm: openssl-devel (Fedora, CentOS, RHEL)
* csw: libssl_dev (Solaris)
* brew: openssl (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘openssl’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/openssl’
* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/XML’
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/RCurl’
ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/httr’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘biomaRt’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/biomaRt’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘rtracklayer’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/rtracklayer’
ERROR: dependency ‘httr’ is not available for package ‘AnnotationHub’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/AnnotationHub’
ERROR: dependencies ‘RCurl’, ‘rtracklayer’, ‘biomaRt’ are not available for package ‘GenomicFeatures’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/GenomicFeatures’
ERROR: dependency ‘rtracklayer’ is not available for package ‘BSgenome’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/BSgenome’
ERROR: dependencies ‘BSgenome’, ‘rtracklayer’, ‘GenomicFeatures’ are not available for package ‘VariantAnnotation’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/VariantAnnotation’
ERROR: dependencies ‘GenomicFeatures’, ‘rtracklayer’, ‘AnnotationHub’ are not available for package ‘ensembldb’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/ensembldb’
ERROR: dependencies ‘GenomicFeatures’, ‘VariantAnnotation’, ‘ensembldb’ are not available for package ‘biovizBase’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/biovizBase’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘GenomicFeatures’, ‘BSgenome’, ‘biovizBase’ are not available for package ‘Gviz’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/Gviz’
ERROR: dependencies ‘rtracklayer’, ‘Gviz’ are not available for package ‘cummeRbund’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/cummeRbund’

The downloaded source packages are in
‘/tmp/RtmpJizAcY/downloaded_packages’
Old packages: 'boot', 'MASS', 'mgcv', 'spatial',
'survival'
Update all/some/none? [a/s/n]:
n
There were 15 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘curl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘openssl’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘XML’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘RCurl’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘httr’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘biomaRt’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘rtracklayer’ had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘AnnotationHub’ had non-zero exit status
9: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘GenomicFeatures’ had non-zero exit status
10: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘BSgenome’ had non-zero exit status
11: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘VariantAnnotation’ had non-zero exit status
12: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘ensembldb’ had non-zero exit status
13: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘biovizBase’ had non-zero exit status
14: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘Gviz’ had non-zero exit status
15: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘cummeRbund’ had non-zero exit status

what should I do to solve this problem???
Any help appreciated

[GenoMax]

Dear all,

I am installing cummeRbund but I am getting the following error;


------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
* deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
* rpm: libcurl-devel (Fedora, CentOS, RHEL)
* csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/curl’
* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
Using PKG_CFLAGS=
Using PKG_LIBS=-lssl -lcrypto
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because openssl was not found. Try installing:
* deb: libssl-dev (Debian, Ubuntu, etc)
* rpm: openssl-devel (Fedora, CentOS, RHEL)
* csw: libssl_dev (Solaris)
* brew: openssl (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘openssl’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/openssl’

Install libcurl and openssl packages for your OS. See help above. What OS are you using?

[k.h]

Install libcurl and openssl packages for your OS. See help above. What OS are you using?

Dear GenoMax,

Thanks for the comment, I am using ubuntu 15.04 LTS. I installed the packages with the command "sudo apt-get install libcurl openssl" but I get the error as below;

Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package libcurl

Then I executed the commands "sudo apt-get install libcurl4-openssl-dev libxml2-dev"
and I get another error;
The following packages have unmet dependencies:
libcurl4-openssl-dev : Depends: libkrb5-dev but it is not going to be installed
Depends: librtmp-dev but it is not going to be installed
Depends: libssl-dev but it is not going to be installed
libxml2-dev : Depends: libxml2 (= 2.9.1+dfsg1-3ubuntu4.8) but 2.9.2+dfsg1-3 is to be installed
E: Unable to correct problems, you have held broken packages.
How could I resolve this problem?

Thanks again for your time

[GenoMax]

You also need to install libkrb5-dev, librtmp-dev and libssl-dev packages based on the messages above.

It may be easier to use the package manager GUI to install and then check the box for install dependencies (if I recollect it right for ubuntu).

[k.h]

You also need to install libkrb5-dev, librtmp-dev and libssl-dev packages based on the messages above.

It may be easier to use the package manager GUI to install and then check the box for install dependencies (if I recollect it right for ubuntu).

Dear GenoMax,

Thanks for the reply, I installed the packages you mentioned above. but it seem the latest version of them are already installed. I am now facing with the following error;

Thanks again.

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
> biocLite("cummeRbund")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘cummeRbund’
also installing the dependencies ‘biovizBase’, ‘Gviz’

trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/biovizBase_1.20.0.tar.gz'
Content type 'unknown' length 2432033 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/Gviz_1.16.1.tar.gz'
Content type 'unknown' length 3387915 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/cummeRbund_2.14.0.tar.gz'
Content type 'unknown' length 2317146 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

* installing *source* package ‘biovizBase’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c R_init_biovizBase.c -o R_init_biovizBase.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bin_offsets.c -o bin_offsets.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/usr/lib/R/lib -lR
installing to /home/k/R/i686-pc-linux-gnu-library/3.3/biovizBase/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: S3 methods ‘[.aareg’, ‘[.Surv’, ‘[.cox.zph’, ‘[.coxph.penalty’, ‘[.ratetable’, ‘[.ratetable2’, ‘[.survfit’, ‘[.survfitms’, ‘[.tcut’, ‘Math.Surv’, ‘Math.ratetable’, ‘Ops.Surv’, ‘Ops.ratetable’, ‘Summary.Surv’, ‘anova.coxph’, ‘anova.coxphlist’, ‘anova.survreg’, ‘anova.survreglist’, ‘as.character.Surv’, ‘as.data.frame.Surv’, ‘as.matrix.ratetable’, ‘as.matrix.Surv’, ‘attrassign.default’, ‘attrassign.lm’, ‘extractAIC.coxph.penal’, ‘dim.survfit’, ‘format.Surv’, ‘is.na.Surv’, ‘is.na.coxph.penalty’, ‘is.na.ratetable’, ‘labels.survreg’, ‘levels.tcut’, ‘lines.aareg’, ‘lines.survexp’, ‘lines.survfit’, ‘logLik.coxph’, ‘logLik.survreg’, ‘makepredictcall.pspline’, ‘model.frame.coxph’, ‘model.frame.survreg’, ‘model.matrix.coxph’, ‘model.matrix.survreg’, ‘plot.aareg’, ‘plot.cox.zph’, ‘plot.survfit’, ‘points.survfit’, ‘ [... truncated]
Error in library.dynam(lib, package, package.lib) :
shared object ‘survival.so’ not found
ERROR: lazy loading failed for package ‘biovizBase’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/biovizBase’
ERROR: dependency ‘biovizBase’ is not available for package ‘Gviz’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/Gviz’
ERROR: dependency ‘Gviz’ is not available for package ‘cummeRbund’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/cummeRbund’

The downloaded source packages are in
‘/tmp/RtmpQHDCcv/downloaded_packages’
Old packages: 'boot', 'MASS', 'spatial', 'survival'
Update all/some/none? [a/s/n]:
a
Warning in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
'lib = "/usr/lib/R/library"' is not writable
Would you like to use a personal library instead? (y/n) y
trying URL 'https://cran.rstudio.com/src/contrib/boot_1.3-18.tar.gz'
Content type 'unknown' length 231831 bytes (226 KB)
==================================================
downloaded 226 KB

trying URL 'https://cran.rstudio.com/src/contrib/MASS_7.3-45.tar.gz'
Content type 'unknown' length 487268 bytes (475 KB)
==================================================
downloaded 475 KB

trying URL 'https://cran.rstudio.com/src/contrib/spatial_7.3-11.tar.gz'
Content type 'unknown' length 44666 bytes (43 KB)
==================================================
downloaded 43 KB

trying URL 'https://cran.rstudio.com/src/contrib/survival_2.39-5.tar.gz'
Content type 'unknown' length 4541205 bytes (4.3 MB)
==================================================
downloaded 4.3 MB

* installing *source* package ‘boot’ ...
** package ‘boot’ successfully unpacked and MD5 sums checked
mv: cannot move ‘/home/k/R/i686-pc-linux-gnu-library/3.3/boot’ to ‘/home/k/R/i686-pc-linux-gnu-library/3.3/00LOCK-boot/boot’: Permission denied
Warning in file.copy(f, instdir, TRUE) :
problem copying ./NAMESPACE to /home/k/R/i686-pc-linux-gnu-library/3.3/boot/NAMESPACE: Permission denied
Warning in file(file, if (append) "a" else "w") :
cannot open file '/home/k/R/i686-pc-linux-gnu-library/3.3/boot/DESCRIPTION': Permission denied
Error in file(file, if (append) "a" else "w") :
cannot open the connection
ERROR: installing package DESCRIPTION failed for package ‘boot’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/boot’
* installing *source* package ‘MASS’ ...
** package ‘MASS’ successfully unpacked and MD5 sums checked
mv: cannot move ‘/home/k/R/i686-pc-linux-gnu-library/3.3/MASS’ to ‘/home/k/R/i686-pc-linux-gnu-library/3.3/00LOCK-MASS/MASS’: Permission denied
Warning in file.copy(f, instdir, TRUE) :
problem copying ./NAMESPACE to /home/k/R/i686-pc-linux-gnu-library/3.3/MASS/NAMESPACE: Permission denied
Warning in file(file, if (append) "a" else "w") :
cannot open file '/home/k/R/i686-pc-linux-gnu-library/3.3/MASS/DESCRIPTION': Permission denied
Error in file(file, if (append) "a" else "w") :
cannot open the connection
ERROR: installing package DESCRIPTION failed for package ‘MASS’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/MASS’
* installing *source* package ‘spatial’ ...
** package ‘spatial’ successfully unpacked and MD5 sums checked
mv: cannot move ‘/home/k/R/i686-pc-linux-gnu-library/3.3/spatial’ to ‘/home/k/R/i686-pc-linux-gnu-library/3.3/00LOCK-spatial/spatial’: Permission denied
Warning in file.copy(f, instdir, TRUE) :
problem copying ./NAMESPACE to /home/k/R/i686-pc-linux-gnu-library/3.3/spatial/NAMESPACE: Permission denied
Warning in file(file, if (append) "a" else "w") :
cannot open file '/home/k/R/i686-pc-linux-gnu-library/3.3/spatial/DESCRIPTION': Permission denied
Error in file(file, if (append) "a" else "w") :
cannot open the connection
ERROR: installing package DESCRIPTION failed for package ‘spatial’
* removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/spatial’
ERROR: failed to lock directory ‘/home/k/R/i686-pc-linux-gnu-library/3.3’ for modifying
Try removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/00LOCK-survival’

The downloaded source packages are in
‘/tmp/RtmpQHDCcv/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘biovizBase’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘Gviz’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘cummeRbund’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
installation of package ‘boot’ had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
installation of package ‘MASS’ had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
installation of package ‘spatial’ had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
installation of package ‘survival’ had non-zero exit status
> library(cummeRbund)
Error in library(cummeRbund) : there is no package called ‘cummeRbund’

[GenoMax]

ERROR: failed to lock directory ‘/home/k/R/i686-pc-linux-gnu-library/3.3’ for modifying
Try removing ‘/home/k/R/i686-pc-linux-gnu-library/3.3/00LOCK-survival’

See if that helps.

[k.h]

See if that helps.

Dear GenoMax,
I realy not know how to remove the "/home/k/R/i686-pc-linux-gnu-library/3.3/00LOCK-survival’"
Could you please provide me the command?

[GenoMax]

rm -f /home/k/R/i686-pc-linux-gnu-library/3.3/00LOCK-survival

In case that does not work then

sudo rm -f /home/k/R/i686-pc-linux-gnu-library/3.3/00LOCK-survival

[k.h]

rm -f /home/k/R/i686-pc-linux-gnu-library/3.3/00LOCK-survival

In case that does not work then

sudo rm -f /home/k/R/i686-pc-linux-gnu-library/3.3/00LOCK-survival

I got the following result. Is that an error?
rm: cannot remove ‘/home/k/R/i686-pc-linux-gnu-library/3.3/00LOCK-survival’: Is a directory

[GenoMax]

I got the following result. Is that an error?
rm: cannot remove ‘/home/k/R/i686-pc-linux-gnu-library/3.3/00LOCK-survival’: Is a directory

Note: While the following will work (it will remove that directory and all files and folders under that directory) I don't have any way of knowing/seeing what is on your machine in that directory (and its sub-dirs). Please consult someone locally if you are unfamiliar with unix.

rm -rf /home/k/R/i686-pc-linux-gnu-library/3.3/00LOCK-survival