CummeRbund installation failing - Page 5

GenoMax · 07-23-2016, 07:28 AM

Quote:

Originally Posted by k.h

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 · 07-24-2016, 11:22 PM

Quote:

Originally Posted by GenoMax

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 · 07-25-2016, 03:31 AM

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 · 07-25-2016, 09:20 AM

Quote:

Originally Posted by 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).

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 · 07-25-2016, 09:22 AM

Quote:

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 · 07-25-2016, 09:26 AM

Quote:

Originally Posted by GenoMax

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 · 07-25-2016, 09:29 AM

Code:

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

In case that does not work then

Code:

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

k.h · 07-25-2016, 09:33 AM

Quote:

Originally Posted by GenoMax

Code:

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

In case that does not work then

Code:

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 · 07-25-2016, 09:48 AM

Quote:

Originally Posted by k.h

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.

Code:

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

k.h · 07-25-2016, 10:33 AM

Quote:

Originally Posted by GenoMax

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.

Code:

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

Dear GenoMax,
Many thanks for your useful suggestions. It worked. Ultimately We (Me and GenoMax) could Install cummeRbund successfully.

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07-25-2016, 09:29 AM	#87
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	Code: rm -f /home/k/R/i686-pc-linux-gnu-library/3.3/00LOCK-survival In case that does not work then Code: sudo rm -f /home/k/R/i686-pc-linux-gnu-library/3.3/00LOCK-survival

07-25-2016, 03:31 AM	#83
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	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).