search

VascoElbrecht / PrimerMiner

R mased batch sequence downloader, with primer development and in silico evaluation capabilities
33 stars 11 forks source link

Error installing JAMP locally #33

Open LarrainK opened 5 years ago

LarrainK commented 5 years ago

Hi Vasco We follow the package_tutorial.R and when we run the following line:

install_github("VascoElbrecht/JAMP", subdir="JAMP")

We obtain the following error:

Downloading GitHub repo VascoElbrecht/JAMP@master tar: Failed to set default locale tar: Failed to set default locale Skipping 1 packages not available: PrimerMiner During startup - Warning messages: 1: Setting LC_CTYPE failed, using "C" 2: Setting LC_TIME failed, using "C" 3: Setting LC_MESSAGES failed, using "C" 4: Setting LC_MONETARY failed, using "C" v checking for file '/private/var/folders/l0/636zb7xd0fg015xw9v4mgt380000gn/T/Rtmpymi7u5/remotes21c51e830429/VascoElbrecht-JAMP-54b0c90/JAMP/DESCRIPTION' ...

Error: (converted from warning) Setting LC_CTYPE failed, using "C" Execution halted Error in i.p(...) : (converted from warning) installation of package '/var/folders/l0/636zb7xd0fg015xw9v4mgt380000gn/T//Rtmpymi7u5/file21c554371e63/JAMP_0.67.tar.gz' had non-zero exit status

And when install install_github("VascoElbrecht/PrimerMiner", subdir="PrimerMiner") We obtain: Downloading GitHub repo VascoElbrecht/PrimerMiner@master tar: Failed to set default locale tar: Failed to set default locale These packages have more recent versions available. Which would you like to update?

1: XML (3.98-1.17 -> 3.98-1.18) [CRAN]

Enter one or more numbers separated by spaces, or an empty line to cancel 1: 1 XML (3.98-1.17 -> 3.98-1.18) [CRAN] Installing 1 packages: XML

There is a binary version available but the source version is later: binary source needs_compilation XML 3.98-1.17 3.98-1.18 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes installing the source package 'XML'

trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.18.tar.gz' Content type 'application/x-gzip' length 1601173 bytes (1.5 MB)

downloaded 1.5 MB

Error: (converted from warning) Setting LC_CTYPE failed, using "C" Execution halted Error in i.p(...) : (converted from warning) installation of package 'XML' had non-zero exit status

Downloading GitHub repo VascoElbrecht/PrimerMiner@master tar: Failed to set default locale tar: Failed to set default locale These packages have more recent versions available. Which would you like to update?

1: XML (3.98-1.17 -> 3.98-1.18) [CRAN]

Enter one or more numbers separated by spaces, or an empty line to cancel 1: 1 XML (3.98-1.17 -> 3.98-1.18) [CRAN] Installing 1 packages: XML

There is a binary version available but the source version is later: binary source needs_compilation XML 3.98-1.17 3.98-1.18 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes installing the source package 'XML'

trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.18.tar.gz' Content type 'application/x-gzip' length 1601173 bytes (1.5 MB)

downloaded 1.5 MB

Error: (converted from warning) Setting LC_CTYPE failed, using "C" Execution halted Error in i.p(...) : (converted from warning) installation of package 'XML' had non-zero exit status

And the package is not installed.

Any suggestion? Thanks

María

VascoElbrecht commented 5 years ago

Hey Maria,

Can you try to install the dependencies first, and see if that solves the issue:

install.packages(c("bold", "XML", "rentrez", "seqinr"), dependencies=T)

best Vasco