Add annotation, biomaRt installation
1
0
Entering edit mode
saida3112 ▴ 10
@saida3112-20263
Last seen 5.8 years ago

Hello,

I want to install biomaRt to add genes annotation after using DESeq2

I use Ubuntu 18.04 & R 3.5

I try

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("biomaRt", version = "3.8")

but it returns different errors:

installation path not writeable, unable to update packages: Matrix
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘openssl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘httr’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘biomaRt’ had non-zero exit status

Thank you.
software error annotation go • 1.9k views
ADD COMMENT •
0
Entering edit mode

I removed DESeq2 tag because it is not relevant.

ADD REPLY •
1
Entering edit mode
Mike Smith ★ 6.6k
@mike-smith
Last seen 2 hours ago
EMBL Heidelberg

I suspect you're missing the OpenSSL system library, and then there's a cascade of missing packages which is preventing you installing biomaRt.

Try running the following in a terminal, and then re-running the BiocManager::install command.

sudo apt-get install libssl-dev libcurl4-openssl-dev

If that doesn't work report back here with a more complete version of the output from the installation.
ADD COMMENT •
0
Entering edit mode

Thank you for your reply, I obtain this outputs (in french) after trying the command line:

    dpkg: libcurl4-gnutls-dev:amd64 : problème de dépendance, mais suppression comme demandé :


libnetcdf-dev dépend de libcurl4-gnutls-dev | libcurl-ssl-dev ; cependant :
  Le paquet libcurl4-gnutls-dev:amd64 doit être supprimé.
  Le paquet libcurl-ssl-dev n'est pas installé.
  Le paquet libcurl4-gnutls-dev:amd64 qui fournit libcurl-ssl-dev doit être supprimé.
 libdap-dev:amd64 dépend de libcurl4-gnutls-dev | libcurl-dev ; cependant :
  Le paquet libcurl4-gnutls-dev:amd64 doit être supprimé.
  Le paquet libcurl-dev n'est pas installé.
  Le paquet libcurl4-gnutls-dev:amd64 qui fournit libcurl-dev doit être supprimé.
 libgdal-dev dépend de libcurl4-gnutls-dev | libcurl-ssl-dev ; cependant :
  Le paquet libcurl4-gnutls-dev:amd64 doit être supprimé.
  Le paquet libcurl-ssl-dev n'est pas installé.
  Le paquet libcurl4-gnutls-dev:amd64 qui fournit libcurl-ssl-dev doit être supprimé.
 libdap-dev:amd64 dépend de libcurl4-gnutls-dev | libcurl-dev ; cependant :
  Le paquet libcurl4-gnutls-dev:amd64 doit être supprimé.
  Le paquet libcurl-dev n'est pas installé.
  Le paquet libcurl4-gnutls-dev:amd64 qui fournit libcurl-dev doit être supprimé.
 libnetcdf-dev dépend de libcurl4-gnutls-dev | libcurl-ssl-dev ; cependant :
  Le paquet libcurl4-gnutls-dev:amd64 doit être supprimé.
  Le paquet libcurl-ssl-dev n'est pas installé.
  Le paquet libcurl4-gnutls-dev:amd64 qui fournit libcurl-ssl-dev doit être supprimé.
 libgdal-dev dépend de libcurl4-gnutls-dev | libcurl-ssl-dev ; cependant :
  Le paquet libcurl4-gnutls-dev:amd64 doit être supprimé.
  Le paquet libcurl-ssl-dev n'est pas installé.
  Le paquet libcurl4-gnutls-dev:amd64 qui fournit libcurl-ssl-dev doit être supprimé.

(Lecture de la base de données... 202734 fichiers et répertoires déjà installés.)
Suppression de libcurl4-gnutls-dev:amd64 (7.58.0-2ubuntu3.6) ...
Sélection du paquet libcurl4-openssl-dev:amd64 précédemment désélectionné.
(Lecture de la base de données... 202712 fichiers et répertoires déjà installés.)
Préparation du dépaquetage de .../libcurl4-openssl-dev_7.58.0-2ubuntu3.6_amd64.deb ...
Dépaquetage de libcurl4-openssl-dev:amd64 (7.58.0-2ubuntu3.6) ...
Sélection du paquet libssl-dev:amd64 précédemment désélectionné.
Préparation du dépaquetage de .../libssl-dev_1.1.0g-2ubuntu4.3_amd64.deb ...
Dépaquetage de libssl-dev:amd64 (1.1.0g-2ubuntu4.3) ...
Sélection du paquet libssl-doc précédemment désélectionné.
Préparation du dépaquetage de .../libssl-doc_1.1.0g-2ubuntu4.3_all.deb ...
Dépaquetage de libssl-doc (1.1.0g-2ubuntu4.3) ...
Paramétrage de libssl-dev:amd64 (1.1.0g-2ubuntu4.3) ...
Traitement des actions différées (« triggers ») pour man-db (2.8.3-2ubuntu0.1) ...
Paramétrage de libssl-doc (1.1.0g-2ubuntu4.3) ...
Paramétrage de libcurl4-openssl-dev:amd64 (7.58.0-2ubuntu3.6) ...

And after re-running the BiocManager::install command I obtain the same outputs :(

ADD REPLY •
0
Entering edit mode

It will help to narrow the problem to the first installation that fails, and to provide additional information. I have

> BiocManager::install("openssl")
Bioconductor version 3.9 (BiocManager 1.30.4), R Under development (unstable)
  (2019-03-06 r76203)
Installing package(s) 'openssl'
trying URL 'https://cran.rstudio.com/src/contrib/openssl_1.2.2.tar.gz'
Content type 'application/x-gzip' length 1196460 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

* installing *source* package 'openssl' ...
** package 'openssl' successfully unpacked and MD5 sums checked
Homebrew 2.0.2
Homebrew/homebrew-core (git revision 4f9cdc; last commit 2019-03-01)
Homebrew/homebrew-cask (git revision c56fb; last commit 2019-02-28)
Using PKG_CFLAGS=-I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/openssl/include
Using PKG_LIBS=-L/usr/local/opt/openssl@1.1/lib -L/usr/local/opt/openssl/lib -lssl.1.1 -lcrypto.1.1
** libs
rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o openssl.so
gcc -I"/Users/ma38727/bin/R-devel/include" -DNDEBUG -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/openssl/include  -I/usr/local/include  -fPIC  -O0 -g -Wall -pedantic -c aes.c -o aes.o
...
gcc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Users/ma38727/bin/R-devel/lib -L/usr/local/lib -o openssl.so aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o -L/usr/local/opt/openssl@1.1/lib -L/usr/local/opt/openssl/lib -lssl.1.1 -lcrypto.1.1 -L/Users/ma38727/bin/R-devel/lib -lR -Wl,-framework -Wl,CoreFoundation
ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation are out of sync. Falling back to library file for linking.
installing to /Users/ma38727/Library/R/3.6/Bioc/3.9/00LOCK-openssl/00new/openssl/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (openssl)

But probably you have an error shrotly after ** package 'openssl' successfully unpacked and MD5 sums checked'

ADD REPLY •
0
Entering edit mode

the output of the used command:

Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘openssl’ had non-zero exit status
ADD REPLY •
0
Entering edit mode

Provide the full output of BiocManager::install("openssl")

ADD REPLY •
0
Entering edit mode
Error: package or namespace load failed for ‘openssl’ in dyn.load(file, DLLpath = DLLpath, ...):

impossible de charger l'objet partagé '/home/saida/R/x8664-pc-linux-gnu-library/3.5/openssl/libs/openssl.so': /usr/lib/x8664-linux-gnu/libcrypto.so.1.1: version `OPENSSL111' not found (required by /home/saida/R/x8664-pc-linux-gnu-library/3.5/openssl/libs/openssl.so) Erreur : le chargement a échoué Exécution arrêtée ERROR: loading failed * removing ‘/home/saida/R/x86_64-pc-linux-gnu-library/3.5/openssl’

The downloaded source packages are in ‘/tmp/RtmpZ5osFD/downloaded_packages’ installation path not writeable, unable to update packages: Matrix, mgcv Update old packages: 'assertthat', 'gtable', 'RBGL', 'RcppArmadillo', 'rlang' Update all/some/none? [a/s/n]:

and after updating old packages I have this output:

Warning message:

In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : installation of package ‘openssl’ had non-zero exit status

ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 646 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6