Error installing JAMP locally

[LarrainK]

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' ...

• preparing 'JAMP':
  v checking DESCRIPTION meta-information ...
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories
• building 'JAMP_0.67.tar.gz'

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]

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