ROracle on R Version 4.0.0 - r

When trying to use ROracle I get the following error message
> library("ROracle")
Error: package or namespace load failed for ‘ROracle’:
package ‘ROracle’ was installed before R 4.0.0: please re-install it
I've installed/downloaded DBI, RTools, oracle isntant client (basic + sdk) and tried following these instructions but it did not work: ROracle install
I'm able to download ROracle just fine (see below) so I'm stumped on what is missing. Do I need to downgrade a version?
> Roracle_path <- "filepath.../ROracle_1.3-2.zip"
> install.packages(Roracle_path, repos = NULL)
Installing package into ‘C:/Users/<my username>/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
package ‘ROracle’ successfully unpacked and MD5 sums checked

ROracle_1.3-2.tar.gz which is built for R 3.6.x works also with R 4.x if you install the package from SOURCES.
On Linux systems at first you have to install the Oracle Instant Client basic and SDK:
/home/jovyan/R
unzip instantclient-basic-linux.x64-21.4.0.0.0dbru.zip -d /opt/oracle/
unzip instantclient-sdk-linux.x64-21.4.0.0.0dbru.zip -d /opt/oracle
The linux package libaio1 have to be installed on the system:
apt install -y libaio1
Next, the environment variables must be set:
export PATH="$PATH:/opt/oracle/instantclient_21_4"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/opt/oracle/instantclient_21_4"
Finally the package can be installed from Sources (use ROracle_1.3-2.tar.gz (sources) but not ROracle_1.3-2_R_x86_64-linux-gnu.tar.gz (binary) ):
R CMD INSTALL --configure-args='--with-oci-lib=/opt/oracle/instantclient_21_4/ --with-oci-inc=/opt/oracle/instantclient_21_4/sdk/include' ROracle_1.3-2.tar.gz
During the installation process you will see that the package will be installed from SOURCES:
* installing to library ‘/opt/conda/lib/R/library’
* installing *source* package ‘ROracle’ ...
** using staged installation
configure: creating ./config.status
config.status: creating src/Makevars
** libs
x86_64-conda-linux-gnu-cc -I"/opt/conda/lib/R/include" -DNDEBUG -I/opt/oracle/instantclient_21_4/sdk/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1639563404388/work=/usr/local/src/conda/r-base-4.1.2 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix -c rodbi.c -o rodbi.o
x86_64-conda-linux-gnu-cc -I"/opt/conda/lib/R/include" -DNDEBUG -I/opt/oracle/instantclient_21_4/sdk/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include -I/opt/conda/include -Wl,-rpath-link,/opt/conda/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1639563404388/work=/usr/local/src/conda/r-base-4.1.2 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix -c rooci.c -o rooci.o
x86_64-conda-linux-gnu-cc -shared -L/opt/conda/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -o ROracle.so rodbi.o rooci.o -L/opt/oracle/instantclient_21_4/ -lclntsh -Wl,-rpath,/opt/oracle/instantclient_21_4/ -L/opt/conda/lib/R/lib -lR
installing to /opt/conda/lib/R/library/00LOCK-ROracle/00new/ROracle/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (ROracle)
#
Check the line in the output to see it will be installed from Sources:
* installing *source* package ‘ROracle’ ...

I downgraded to R 3.6.3 and used RTools 35 and now it works.

Related

R package RcppArmadillo "has a configure script" and "probably needs manual configuration"

I just updated my R packages packages in RStudio. For the RcppArmadillo package (version 0.11.4.3.1), RStudio warned me that no binary package is available for my system (x86_64, Windows 11) and asked if I wanted to install the source package instead. Since I have RTools installed for just this purpose, I said yes.
The installation succeeded, but a warning was issued that the package "has a configure script" and "probably needs manual configuration".
* installing *source* package 'RcppArmadillo' ...
** package 'RcppArmadillo' successfully unpacked and MD5 sums checked
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I'C:/.../R/win-library/4.2/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -I../inst/include -I. -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppArmadillo.cpp -o RcppArmadillo.o
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I'C:/.../R/win-library/4.2/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -I../inst/include -I. -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I'C:/.../R/win-library/4.2/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -I../inst/include -I. -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fastLm.cpp -o fastLm.o
g++ -shared -s -static-libgcc -o RcppArmadillo.dll tmp.def RcppArmadillo.o RcppExports.o fastLm.o -fopenmp -LC:/PROGRA~1/R/R-42~1.2/bin/x64 -lRlapack -LC:/PROGRA~1/R/R-42~1.2/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA~1/R/R-42~1.2/bin/x64 -lR
installing to C:/.../R/win-library/4.2/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RcppArmadillo)
My questions are:
Should I be concerned?
How can I tell that the package is working correctly?
If manual configuration is needed, how do I do it?
An aside for the second of those: I'm not using this package directly, and presume that it was installed as a dependency of another package that I used in the past. Since I do not remember which package that may have been (or when I last used it), I can't just dig into my older code, find a script that uses this package, and see if it still works.
Is there such a thing in the R world as automated tests to ensure that a newly-compiled package actually works before it gets installed? I'm a little surprised that this is apparently not done by default.

Installing R package `MatchIt` in Anaconda Environment [duplicate]

This question already has answers here:
How to install R packages that are not available in "R-essentials"?
(11 answers)
Closed last year.
I am attempting to install MatchIt - an R package - in an Anaconda environment. I keep getting error messages that I just don't understand.
I made sure that I had Rcpp installed in the same Conda environment and that I have Xcode installed on my machine. Still no luck. I was wondering if anyone had a solution.
devtools::install_github('kosukeimai/MatchIt')
Downloading GitHub repo kosukeimai/MatchIt#HEAD
✔ checking for file ‘/private/var/folders/cz/1d4gc7b13dsfknrnbr0tjz580000gn/T/RtmpYISSL1/remotes50d505ff397/kosukeimai-MatchIt-b3032e6/DESCRIPTION’ ...
─ preparing ‘MatchIt’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ installing the package to process help pages
-----------------------------------
─ installing *source* package ‘MatchIt’ ...
** using staged installation
** libs
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/opt/anaconda3/envs/pirate/lib/R/include" -DNDEBUG -I'/opt/anaconda3/envs/pirate/lib/R/library/Rcpp/include' -I'/opt/anaconda3/envs/pirate/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem /opt/anaconda3/envs/pirate/include -mmacosx-version-min=10.9 -I/opt/anaconda3/envs/pirate/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /opt/anaconda3/envs/pirate/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1630154249442/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/opt/anaconda3/envs/pirate=/usr/local/src/conda-prefix -Wall -pedantic -c RcppExports.cpp -o RcppExports.o
/bin/sh: x86_64-apple-darwin13.4.0-clang++: command not found
make: *** [RcppExports.o] Error 127
ERROR: compilation failed for package ‘MatchIt’
─ removing ‘/private/var/folders/cz/1d4gc7b13dsfknrnbr0tjz580000gn/T/RtmpeKesPi/Rinst1a5f6063566d/MatchIt’
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'MatchIt' from GitHub:
System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E> * installing *source* package ‘MatchIt’ ...
E> ** using staged installation
E> ** libs
E> x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/opt/anaconda3/envs/pirate/lib/R/include" -DNDEBUG -I'/opt/anaconda3/envs/pirate/lib/R/library/Rcpp/include' -I'/opt/anaconda3/envs/pirate/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem /opt/anaconda3/envs/pirate/include -mmacosx-version-min=10.9 -I/opt/anaconda3/envs/pirate/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /opt/anaconda3/envs/pirate/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1630154249442/work=/usr/local/src/conda/r-base-4.1.1 -fdebug-prefix-map=/opt/anaconda3/envs/pirate=/usr/local/src/conda-prefix -Wall -pedant
I have also looked around on the Conda-forge channel to see if I could just conda install -c conda-forge r-MatchIt but no luck either.
I ended up getting the package to install and compile but I am not exactly sure how.
I deleted then reinstalled Xcode.
I then accessed R in my conda environment via terminal and tried reinstalling the package that way with pgkbuild().
$ conda activate pirate
$ R
> pkgbuild::check_build_tools(devtools::install_github('kosukeimai/MatchIt'), debug = TRUE)
I obviously don't really understand how any of the Clang compiling works, but if this can be useful for someone as clueless as I am, I guess the ole classic of deleting and reinstalling Xcode will do it.

Shared .so file not found when loading R package with Rcpp component Linux systems

I apologize in advance if this question has been asked before but I haven't been able to find a suitable answer after days of searching.
I have a package that has a couple of small functions written in C++ using Rcpp (package can be found here). When trying to install this package on Linux systems (both local install and via Github Actions - Ubuntu 18.04, 20.04) the compiling procedure was successful but R cannot load the package because an .so file was not found. Mac and Windows systems work fine and there were no R CMD CHECK issues when tested on these systems.
I was wondering if there is any way to solve this issue? I was thinking of adding something in .Makevars but I don't know what to add.
Thank you so much in advance.
─ installing *source* package ‘CBEA’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I'/__w/_temp/Library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -pedantic -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I'/__w/_temp/Library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -pedantic -c gmeans.cpp -o gmeans.o
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o CBEA.so RcppExports.o gmeans.o -L/usr/local/lib/R/lib -lR
installing to /tmp/RtmpwFufM0/Rinst8982598ffd0c/00LOCK-CBEA/00new/CBEA/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘CBEA’ in library.dynam(lib, package, package.lib):
shared object ‘cbea.so’ not found
Error: loading failed
Execution halted
ERROR: loading failed
─ removing ‘/tmp/RtmpwFufM0/Rinst8982598ffd0c/CBEA’
Your (generated) NAMESPACE file has two entries referring to the package:
useDynLib(CBEA, .registration = TRUE)
useDynLib(cbea, .registration = TRUE)
Remove the second one (i.e. remove whereever you tell roxygen2 to add it, and you will be fine. The rror message you see and quote indicates a case issue as on Linux, cbea.so is different from CBEA.so (whereas macOS and Windows let you get away with it).

How to install odbc package to Databricks cluster?

I need to access an Azure SQL Database from an R notebook in Databricks. To do this I aimed to use the odbc package, which installed fine on my local instance of R.
I have tried to install the package to the cluster using Databricks' interface, which always fails. I have also tried the following code within a notebook:
install.packages("odbc")
which results in:
Installing package into ‘/databricks/spark/R/lib’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/odbc_1.1.6.tar.gz'
Content type 'application/x-gzip' length 288033 bytes (281 KB)
==================================================
downloaded 281 KB
* installing *source* package ‘odbc’ ...
** package ‘odbc’ successfully unpacked and MD5 sums checked
PKG_CFLAGS=
PKG_LIBS=-lodbc
<stdin>:1:17: fatal error: sql.h: No such file or directory
compilation terminated.
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because odbc was not found. Try installing:
* deb: unixodbc-dev (Debian, Ubuntu, etc)
* rpm: unixODBC-devel (Fedora, CentOS, RHEL)
* csw: unixodbc_dev (Solaris)
* brew: unixodbc (Mac OSX)
To use a custom odbc set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘odbc’
* removing ‘/databricks/spark/R/lib/odbc’
The downloaded source packages are in
‘/tmp/RtmpqHp2QM/downloaded_packages’
I have also tried installing from github:
library(devtools)
devtools::install_github("r-dbi/odbc")
Which gives a different error:
Downloading GitHub repo r-dbi/odbc#master
Installing 3 packages: assertthat, BH, Rcpp
Installing packages into ‘/databricks/spark/R/lib’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/assertthat_0.2.1.tar.gz'
Content type 'application/x-gzip' length 12742 bytes (12 KB)
==================================================
downloaded 12 KB
trying URL 'https://cloud.r-project.org/src/contrib/BH_1.69.0-1.tar.gz'
Content type 'application/x-gzip' length 12378154 bytes (11.8 MB)
==================================================
downloaded 11.8 MB
trying URL 'https://cloud.r-project.org/src/contrib/Rcpp_1.0.1.tar.gz'
Content type 'application/x-gzip' length 3661123 bytes (3.5 MB)
==================================================
downloaded 3.5 MB
* installing *source* package ‘assertthat’ ...
** package ‘assertthat’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (assertthat)
* installing *source* package ‘BH’ ...
** package ‘BH’ successfully unpacked and MD5 sums checked
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BH)
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Date.cpp -o Date.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Module.cpp -o Module.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rcpp_init.cpp -o Rcpp_init.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api.cpp -o api.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c attributes.cpp -o attributes.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c barrier.cpp -o barrier.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/usr/lib/R/lib -lR
installing to /databricks/spark/R/lib/Rcpp/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rcpp)
The downloaded source packages are in
‘/tmp/RtmpqHp2QM/downloaded_packages’
Error in processx::run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout), :
System command error
In addition: Warning messages:
1: In install.packages("odbc") :
installation of package ‘odbc’ had non-zero exit status
2: In install.packages("odbc") :
installation of package ‘odbc’ had non-zero exit status
Any idea why this package will not install on Databricks when it works fine locally and when all other packages I have tried install on Databricks work fine using the same syntax?
Best option to access a SQL Database is using the preinstalled JDBC connectivity (see the Documentation).
If you want to use ODBC this requires (as mentioned in one of the comments) unix odbc. Good practice to install multiple packages is using init-scripts. Following python code is for creating an init-script for pyodbc installation.
script = """
sudo apt-get -q -y install unixodbc unixodbc-dev
sudo apt-get -q -y install python3-dev
sudo pip install pyodbc
curl https://packages.microsoft.com/keys/microsoft.asc | apt-key add -
sudo curl https://packages.microsoft.com/config/ubuntu/16.04/prod.list > /etc/apt/sources.list.d/mssql-release.list
sudo apt-get update
sudo ACCEPT_EULA=Y apt-get -q -y install msodbcsql
"""
dbutils.fs.put("/databricks/init/pyodbc/pyodbc.sh", script, True)
Hope this helps.

compiling R package on ubuntu, invalid ELF header

I am no longer able to compile an R package from source, and this has never been a problem before today. This is what happens:
R CMD build BAMMtools
* checking for file ‘BAMMtools/DESCRIPTION’ ... OK
* preparing ‘BAMMtools’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘BAMMtools_2.1.0.tar.gz’
R CMD INSTALL BAMMtools
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘BAMMtools’ ...
** libs
make: Nothing to be done for 'all'.
installing to /usr/local/lib/R/site-library/BAMMtools/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/lib/R/site-library/BAMMtools/libs/BAMMtools.so':
/usr/local/lib/R/site-library/BAMMtools/libs/BAMMtools.so: invalid ELF header
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/BAMMtools’
* restoring previous ‘/usr/local/lib/R/site-library/BAMMtools’
This does not seem to be a problem with this R package in particular, as I am able to install the package from within R, as:
> install.packages('BAMMtools_2.1.0.tar.gz', repos=NULL)
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘BAMMtools’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c cohort_matrix.c -o cohort_matrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c dtrates.c -o dtrates.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c jenksBrks.c -o jenksBrks.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c treetraverse.c -o treetraverse.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o BAMMtools.so cohort_matrix.o dtrates.o jenksBrks.o treetraverse.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/BAMMtools/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BAMMtools)
I am running R v3.2.2, under Ubuntu v15.10 wily. I can't think of anything I've done within the last 24 hours that would have this effect, except updating my system with sudo apt-get update/upgrade.
Although this is not too much of a problem for installing the package, I can't run the R CMD check commands either, and this is a problem for development.
Any suggestions or advice would be greatly appreciated! Thanks!
As was found in the comments to the question, thanks to Jack Wasey, the problem was simply that I was running R CMD INSTALL on the name of the source directory, rather than on the built .tar.gz file.

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