Add annotation, biomaRt installation
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saida3112 ▴ 10
@saida3112-20263
Last seen 5.1 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 • 1.6k views
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I removed DESeq2 tag because it is not relevant.

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Mike Smith ★ 6.5k
@mike-smith
Last seen 12 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.
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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 :(

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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'

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

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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

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