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SticsRPacks / CroptimizR

Estimate Crop Models' parameters
https://sticsrpacks.github.io/CroptimizR/
GNU Lesser General Public License v3.0
23 stars 6 forks source link

Cyclic dependencies? #5

Closed hol430 closed 4 years ago

hol430 commented 4 years ago

Unable to install package

Hi all, I'm having some trouble installing the package on a new machine today:

Expected Behavior

I can install the package

Current Behavior

Unable to install the package

Failure Information (for bugs)

There seems to be a cyclic dependency between this package (CroptimizR) and SticksRPacks. These two packages both list the other in their DESCRIPTION file. No idea if this is a good or bad thing in R.

Example:

R code: 

devtools::install_github('SticsRPacks/CroptimizR', lib = '~/.local/share/ApsimInitiative/ApsimX/rpackages', dependencies = TRUE)

Output (note that this is being exeucted by another tool (apsim), so the stdout and stderr are separated):


Error from R:
Script path: '/tmp/a30d33a5-54f4-45f9-aef9-78802ff7c041-InstallGithubPackage.r'
StdErr:
Downloading GitHub repo SticsRPacks/CroptimizR@HEAD
Downloading GitHub repo SticsRPacks/SticsRPacks@HEAD
Downloading GitHub repo SticsRPacks/SticsOnR@v0.1.0.9005
Installing 18 packages: iterators, colorspace, viridisLite, RColorBrewer, munsell, labeling, farver, foreach, plyr, scales, isoband, gtable, XML, doParallel, dfoptim, reshape2, ggplot2, data.table
trying URL 'https://cloud.r-project.org/src/contrib/iterators_1.0.12.tar.gz'
Content type 'application/x-gzip' length 289201 bytes (282 KB)
==================================================
downloaded 282 KB
trying URL 'https://cloud.r-project.org/src/contrib/colorspace_1.4-1.tar.gz'
Content type 'application/x-gzip' length 2152594 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
trying URL 'https://cloud.r-project.org/src/contrib/viridisLite_0.3.0.tar.gz'
Content type 'application/x-gzip' length 44019 bytes (42 KB)
==================================================
downloaded 42 KB
trying URL 'https://cloud.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz'
Content type 'application/x-gzip' length 11532 bytes (11 KB)
==================================================
downloaded 11 KB
trying URL 'https://cloud.r-project.org/src/contrib/munsell_0.5.0.tar.gz'
Content type 'application/x-gzip' length 182653 bytes (178 KB)
==================================================
downloaded 178 KB
trying URL 'https://cloud.r-project.org/src/contrib/labeling_0.3.tar.gz'
Content type 'application/x-gzip' length 10722 bytes (10 KB)
==================================================
downloaded 10 KB
trying URL 'https://cloud.r-project.org/src/contrib/farver_2.0.3.tar.gz'
Content type 'application/x-gzip' length 1279579 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'https://cloud.r-project.org/src/contrib/foreach_1.5.0.tar.gz'
Content type 'application/x-gzip' length 87370 bytes (85 KB)
==================================================
downloaded 85 KB
trying URL 'https://cloud.r-project.org/src/contrib/plyr_1.8.6.tar.gz'
Content type 'application/x-gzip' length 401191 bytes (391 KB)
==================================================
downloaded 391 KB
trying URL 'https://cloud.r-project.org/src/contrib/scales_1.1.1.tar.gz'
Content type 'application/x-gzip' length 515201 bytes (503 KB)
==================================================
downloaded 503 KB
trying URL 'https://cloud.r-project.org/src/contrib/isoband_0.2.2.tar.gz'
Content type 'application/x-gzip' length 2295931 bytes (2.2 MB)
==================================================
downloaded 2.2 MB
trying URL 'https://cloud.r-project.org/src/contrib/gtable_0.3.0.tar.gz'
Content type 'application/x-gzip' length 368081 bytes (359 KB)
==================================================
downloaded 359 KB
trying URL 'https://cloud.r-project.org/src/contrib/XML_3.99-0.5.tar.gz'
Content type 'application/x-gzip' length 968563 bytes (945 KB)
==================================================
downloaded 945 KB
trying URL 'https://cloud.r-project.org/src/contrib/doParallel_1.0.15.tar.gz'
Content type 'application/x-gzip' length 173578 bytes (169 KB)
==================================================
downloaded 169 KB
trying URL 'https://cloud.r-project.org/src/contrib/dfoptim_2018.2-1.tar.gz'
Content type 'application/x-gzip' length 10010 bytes
==================================================
downloaded 10010 bytes
trying URL 'https://cloud.r-project.org/src/contrib/reshape2_1.4.4.tar.gz'
Content type 'application/x-gzip' length 37307 bytes (36 KB)
==================================================
downloaded 36 KB
trying URL 'https://cloud.r-project.org/src/contrib/ggplot2_3.3.2.tar.gz'
Content type 'application/x-gzip' length 3054431 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
trying URL 'https://cloud.r-project.org/src/contrib/data.table_1.13.0.tar.gz'
Content type 'application/x-gzip' length 5273400 bytes (5.0 MB)
==================================================
downloaded 5.0 MB
* installing *source* package ‘iterators’ ...
** package ‘iterators’ successfully unpacked and MD5 sums checked
** using staged installation
** 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 (iterators)
* installing *source* package ‘colorspace’ ...
** package ‘colorspace’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
installing to /home/drew/.config/ApsimInitiative/ApsimX/rpackages/00LOCK-colorspace/00new/colorspace/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** 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 (colorspace)
* installing *source* package ‘viridisLite’ ...
** package ‘viridisLite’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** 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 (viridisLite)
* installing *source* package ‘RColorBrewer’ ...
** package ‘RColorBrewer’ successfully unpacked and MD5 sums checked
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RColorBrewer)
* installing *source* package ‘labeling’ ...
** package ‘labeling’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (labeling)
* installing *source* package ‘farver’ ...
** package ‘farver’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
installing to /home/drew/.config/ApsimInitiative/ApsimX/rpackages/00LOCK-farver/00new/farver/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (farver)
* installing *source* package ‘plyr’ ...
** package ‘plyr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
installing to /home/drew/.config/ApsimInitiative/ApsimX/rpackages/00LOCK-plyr/00new/plyr/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (plyr)
* installing *source* package ‘isoband’ ...
** package ‘isoband’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
installing to /home/drew/.config/ApsimInitiative/ApsimX/rpackages/00LOCK-isoband/00new/isoband/libs
** R
** 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
** 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 (isoband)
* installing *source* package ‘gtable’ ...
** package ‘gtable’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gtable)
* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
installing to /home/drew/.config/ApsimInitiative/ApsimX/rpackages/00LOCK-XML/00new/XML/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 (XML)
* installing *source* package ‘dfoptim’ ...
** package ‘dfoptim’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (dfoptim)
* installing *source* package ‘data.table’ ...
** package ‘data.table’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
installing to /home/drew/.config/ApsimInitiative/ApsimX/rpackages/00LOCK-data.table/00new/data.table/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 (data.table)
* installing *source* package ‘munsell’ ...
** package ‘munsell’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** 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 (munsell)
* installing *source* package ‘foreach’ ...
** package ‘foreach’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** 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 (foreach)
* installing *source* package ‘reshape2’ ...
** package ‘reshape2’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
installing to /home/drew/.config/ApsimInitiative/ApsimX/rpackages/00LOCK-reshape2/00new/reshape2/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (reshape2)
* installing *source* package ‘scales’ ...
** package ‘scales’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** 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 (scales)
* installing *source* package ‘doParallel’ ...
** package ‘doParallel’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** 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 (doParallel)
* installing *source* package ‘ggplot2’ ...
** package ‘ggplot2’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ggplot2)
The downloaded source packages are in
    ‘/tmp/RtmpNDokTl/downloaded_packages’
* installing *source* package ‘SticsOnR’ ...
** using staged installation
** 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 (SticsOnR)
Downloading GitHub repo SticsRPacks/CroptimizR@v0.1.0.9003
Skipping CroptimizR, it is already being installed
Downloading GitHub repo SticsRPacks/SticsRFiles@v0.1.0.9004
Installing 6 packages: hms, progress, cellranger, readxl, xslt, lubridate
trying URL 'https://cloud.r-project.org/src/contrib/hms_0.5.3.tar.gz'
Content type 'application/x-gzip' length 134669 bytes (131 KB)
==================================================
downloaded 131 KB
trying URL 'https://cloud.r-project.org/src/contrib/progress_1.2.2.tar.gz'
Content type 'application/x-gzip' length 29506 bytes (28 KB)
==================================================
downloaded 28 KB
trying URL 'https://cloud.r-project.org/src/contrib/cellranger_1.1.0.tar.gz'
Content type 'application/x-gzip' length 63857 bytes (62 KB)
==================================================
downloaded 62 KB
trying URL 'https://cloud.r-project.org/src/contrib/readxl_1.3.1.tar.gz'
Content type 'application/x-gzip' length 2056165 bytes (2.0 MB)
==================================================
downloaded 2.0 MB
trying URL 'https://cloud.r-project.org/src/contrib/xslt_1.4.2.tar.gz'
Content type 'application/x-gzip' length 17577 bytes (17 KB)
==================================================
downloaded 17 KB
trying URL 'https://cloud.r-project.org/src/contrib/lubridate_1.7.9.tar.gz'
Content type 'application/x-gzip' length 467131 bytes (456 KB)
==================================================
downloaded 456 KB
* installing *source* package ‘hms’ ...
** package ‘hms’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** 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 (hms)
* installing *source* package ‘cellranger’ ...
** package ‘cellranger’ successfully unpacked and MD5 sums checked
** using staged installation
** 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 (cellranger)
* installing *source* package ‘xslt’ ...
** package ‘xslt’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
installing to /home/drew/.config/ApsimInitiative/ApsimX/rpackages/00LOCK-xslt/00new/xslt/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 (xslt)
* installing *source* package ‘lubridate’ ...
** package ‘lubridate’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
installing to /home/drew/.config/ApsimInitiative/ApsimX/rpackages/00LOCK-lubridate/00new/lubridate/libs
** R
** data
*** moving datasets to lazyload DB
** 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
** 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 (lubridate)
* installing *source* package ‘progress’ ...
** package ‘progress’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** 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 (progress)
* installing *source* package ‘readxl’ ...
** package ‘readxl’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
installing to /home/drew/.config/ApsimInitiative/ApsimX/rpackages/00LOCK-readxl/00new/readxl/libs
** R
** 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
** 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 (readxl)
The downloaded source packages are in
    ‘/tmp/RtmpNDokTl/downloaded_packages’
* installing *source* package ‘SticsRFiles’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (SticsRFiles)
Skipping install of 'SticsOnR' from a github remote, the SHA1 (c7033eab) has not changed since last install.
  Use `force = TRUE` to force installation
Downloading GitHub repo SticsRPacks/CroptimizR@v0.1.0.9003
Skipping CroptimizR, it is already being installed
Skipping install of 'SticsRFiles' from a github remote, the SHA1 (4de731c2) has not changed since last install.
  Use `force = TRUE` to force installation
ERROR: dependency ‘CroptimizR’ is not available for package ‘SticsRPacks’
* removing ‘/home/drew/.config/ApsimInitiative/ApsimX/rpackages/SticsRPacks’
Error: Failed to install 'CroptimizR' from GitHub:
  Failed to install 'SticsRPacks' from GitHub:
  (converted from warning) installation of package ‘/tmp/RtmpNDokTl/file1089c747ba6be/SticsRPacks_0.0.1.9000.tar.gz’ had non-zero exit status
Execution halted

StdOut:
SticsRPacks  (NA -> cf1bd2a8c...) [GitHub]
iterators    (NA -> 1.0.12      ) [CRAN]
zoo          (NA -> 1.8-8       ) [CRAN]
intervals    (NA -> 0.15.2      ) [CRAN]
plyr         (NA -> 1.8.6       ) [CRAN]
FNN          (NA -> 1.1.3       ) [CRAN]
spacetime    (NA -> 1.2-3       ) [CRAN]
reshape      (NA -> 0.8.8       ) [CRAN]
maptools     (NA -> 1.0-2       ) [CRAN]
sp           (NA -> 1.4-2       ) [CRAN]
automap      (NA -> 1.0-14      ) [CRAN]
gstat        (NA -> 2.0-6       ) [CRAN]
e1071        (NA -> 1.7-3       ) [CRAN]
xts          (NA -> 0.12-0      ) [CRAN]
colorspace   (NA -> 1.4-1       ) [CRAN]
viridisLite  (NA -> 0.3.0       ) [CRAN]
RColorBrewer (NA -> 1.1-2       ) [CRAN]
munsell      (NA -> 0.5.0       ) [CRAN]
labeling     (NA -> 0.3         ) [CRAN]
farver       (NA -> 2.0.3       ) [CRAN]
scales       (NA -> 1.1.1       ) [CRAN]
coda         (NA -> 0.19-3      ) [CRAN]
Brobdingnag  (NA -> 1.2-6       ) [CRAN]
mvtnorm      (NA -> 1.1-1       ) [CRAN]
statmod      (NA -> 1.4.34      ) [CRAN]
minqa        (NA -> 1.2.4       ) [CRAN]
RcppEigen    (NA -> 0.3.3.7.0   ) [CRAN]
TMB          (NA -> 1.7.18      ) [CRAN]
glmmTMB      (NA -> 1.0.2.1     ) [CRAN]
lme4         (NA -> 1.1-23      ) [CRAN]
qgam         (NA -> 1.3.2       ) [CRAN]
sfsmisc      (NA -> 1.1-7       ) [CRAN]
ape          (NA -> 5.4-1       ) [CRAN]
lmtest       (NA -> 0.9-37      ) [CRAN]
gap          (NA -> 1.2.2       ) [CRAN]
foreach      (NA -> 1.5.0       ) [CRAN]
doParallel   (NA -> 1.0.15      ) [CRAN]
expm         (NA -> 0.999-5     ) [CRAN]
sandwich     (NA -> 2.5-1       ) [CRAN]
gmm          (NA -> 1.6-5       ) [CRAN]
hydroTSM     (NA -> 0.6-0       ) [CRAN]
gtable       (NA -> 0.3.0       ) [CRAN]
isoband      (NA -> 0.2.2       ) [CRAN]
bridgesam... (NA -> 1.0-0       ) [CRAN]
DHARMa       (NA -> 0.3.2.0     ) [CRAN]
msm          (NA -> 1.6.8       ) [CRAN]
numDeriv     (NA -> 2016.8-1.1  ) [CRAN]
ellipse      (NA -> 0.4.2       ) [CRAN]
IDPmisc      (NA -> 1.1.20      ) [CRAN]
tmvtnorm     (NA -> 1.4-10      ) [CRAN]
emulator     (NA -> 1.2-20      ) [CRAN]
hydroGOF     (NA -> 0.4-0       ) [CRAN]
gridExtra    (NA -> 2.3         ) [CRAN]
ggplot2      (NA -> 3.3.2       ) [CRAN]
tictoc       (NA -> 1.0         ) [CRAN]
lubridate    (NA -> 1.7.9       ) [CRAN]
BayesianT... (NA -> 0.1.7       ) [CRAN]
SticsOnR    (NA -> c7033eabb...) [GitHub]
CroptimizR  (NA -> 8b6cea67c...) [GitHub]
SticsRFiles (NA -> 4de731c20...) [GitHub]
iterators    (NA -> 1.0.12  ) [CRAN]
colorspace   (NA -> 1.4-1   ) [CRAN]
viridisLite  (NA -> 0.3.0   ) [CRAN]
RColorBrewer (NA -> 1.1-2   ) [CRAN]
munsell      (NA -> 0.5.0   ) [CRAN]
labeling     (NA -> 0.3     ) [CRAN]
farver       (NA -> 2.0.3   ) [CRAN]
foreach      (NA -> 1.5.0   ) [CRAN]
plyr         (NA -> 1.8.6   ) [CRAN]
scales       (NA -> 1.1.1   ) [CRAN]
isoband      (NA -> 0.2.2   ) [CRAN]
gtable       (NA -> 0.3.0   ) [CRAN]
XML          (NA -> 3.99-0.5) [CRAN]
doParallel   (NA -> 1.0.15  ) [CRAN]
dfoptim      (NA -> 2018.2-1) [CRAN]
reshape2     (NA -> 1.4.4   ) [CRAN]
ggplot2      (NA -> 3.3.2   ) [CRAN]
data.table   (NA -> 1.13.0  ) [CRAN]
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c colorspace.c -o colorspace.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c init.c -o init.o
gcc -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o colorspace.so colorspace.o init.o -L/usr/lib64/R/lib -lR
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c ColorSpace.cpp -o ColorSpace.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c Comparison.cpp -o Comparison.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c Conversion.cpp -o Conversion.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c encode.cpp -o encode.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c farver.cpp -o farver.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c init.cpp -o init.o
g++ -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o farver.so ColorSpace.o Comparison.o Conversion.o encode.o farver.o init.o -L/usr/lib64/R/lib -lR
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG  -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c RcppExports.cpp -o RcppExports.o
gcc -I"/usr/include/R/" -DNDEBUG  -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c loop_apply.c -o loop_apply.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG  -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c split-numeric.cpp -o split-numeric.o
g++ -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o plyr.so RcppExports.o loop_apply.o split-numeric.o -L/usr/lib64/R/lib -lR
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG  -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/testthat/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c clip-lines.cpp -o clip-lines.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG  -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/testthat/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c init.cpp -o init.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG  -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/testthat/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c isoband.cpp -o isoband.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG  -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/testthat/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c polygon.cpp -o polygon.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG  -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/testthat/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c separate-polygons.cpp -o separate-polygons.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG  -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/testthat/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c test-clip-lines.cpp -o test-clip-lines.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG  -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/testthat/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG  -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/testthat/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c test-separate-polygons.cpp -o test-separate-polygons.o
g++ -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o isoband.so clip-lines.o init.o isoband.o polygon.o separate-polygons.o test-clip-lines.o test-runner.o test-separate-polygons.o -L/usr/lib64/R/lib -lR
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /usr/bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... /usr/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -E
Minor 9, Patch 10 for 2.9.10
Located parser file -I/usr/include/libxml2/parser.h
Checking for 1.8:  -I/usr/include/libxml2
Using libxml2.*
checking for gzopen in -lz... yes
checking for xmlParseFile in -lxml2... yes
checking for xmlHashSize in -lxml2... yes
Using built-in xmlHashSize
Checking DTD parsing (presence of externalSubset)...
checking for xmlHashSize in -lxml2... yes
Found xmlHashSize
checking for xmlOutputBufferCreateBuffer in -lxml2... yes
have xmlOutputBufferCreateBuffer()
checking for xmlDocDumpFormatMemoryEnc in -lxml2... yes
checking libxml/xmlversion.h usability... yes
checking libxml/xmlversion.h presence... yes
checking for libxml/xmlversion.h... yes
Expat:  FALSE
Checking for return type of xmlHashScan element routine.
No return value for xmlHashScan
xmlNs has a context field
Checking for cetype_t enumeration
No cetype_t enumeration defined in R headers.
checking for xmlsec1-config... /usr/bin/xmlsec1-config
nodegc default 
xml-debug default 
Version has XML_WITH_ZLIB
Version has xmlHasFeature()
****************************************
Configuration information:
Libxml settings
libxml include directory: -I/usr/include/libxml2
libxml library directory: -lxml2 -lz -llzma -licui18n -licuuc -licudata -lm -ldl -lz  -lxml2
libxml 2:                 -DLIBXML2=1
Compilation flags:         -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1
Link flags:               -lxml2 -lz -llzma -licui18n -licuuc -licudata -lm -ldl -lz  -lxml2 -L/usr/lib -lltdl -lxmlsec1 -lz -llzma -licui18n -licuuc -licudata -ldl -lxslt -lxml2 -lm
****************************************
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/supports.R
config.status: creating inst/scripts/RSXML.csh
config.status: creating inst/scripts/RSXML.bsh
gcc -I"/usr/include/R/" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1  -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c DocParse.c -o DocParse.o
gcc -I"/usr/include/R/" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1  -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c EventParse.c -o EventParse.o
gcc -I"/usr/include/R/" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1  -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c ExpatParse.c -o ExpatParse.o
gcc -I"/usr/include/R/" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1  -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c HTMLParse.c -o HTMLParse.o
gcc -I"/usr/include/R/" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1  -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c NodeGC.c -o NodeGC.o
gcc -I"/usr/include/R/" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1  -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c RSDTD.c -o RSDTD.o
gcc -I"/usr/include/R/" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1  -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c RUtils.c -o RUtils.o
gcc -I"/usr/include/R/" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1  -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c Rcatalog.c -o Rcatalog.o
gcc -I"/usr/include/R/" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1  -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c Utils.c -o Utils.o
gcc -I"/usr/include/R/" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1  -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c XMLEventParse.c -o XMLEventParse.o
gcc -I"/usr/include/R/" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1  -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c XMLHashTree.c -o XMLHashTree.o
gcc -I"/usr/include/R/" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1  -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c XMLTree.c -o XMLTree.o
gcc -I"/usr/include/R/" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1  -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c fixNS.c -o fixNS.o
gcc -I"/usr/include/R/" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1  -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c libxmlFeatures.c -o libxmlFeatures.o
gcc -I"/usr/include/R/" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1  -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c schema.c -o schema.o
gcc -I"/usr/include/R/" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1  -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c xmlsecurity.c -o xmlsecurity.o
gcc -I"/usr/include/R/" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_DL_LIBLTDL=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1  -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c xpath.c -o xpath.o
gcc -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o XML.so DocParse.o EventParse.o ExpatParse.o HTMLParse.o NodeGC.o RSDTD.o RUtils.o Rcatalog.o Utils.o XMLEventParse.o XMLHashTree.o XMLTree.o fixNS.o libxmlFeatures.o schema.o xmlsecurity.o xpath.o -lxml2 -lz -llzma -licui18n -licuuc -licudata -lm -ldl -lz -lxml2 -L/usr/lib -lltdl -lxmlsec1 -lz -llzma -licui18n -licuuc -licudata -ldl -lxslt -lxml2 -lm -L/usr/lib64/R/lib -lR
Creating a generic function for ‘source’ from package ‘base’ in package ‘XML’
in method for ‘xmlAttrsToDataFrame’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘readKeyValueDB’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘readSolrDoc’ with signature ‘"AsIs"’: no definition for class “AsIs”
gcc 10.2.0
zlib 1.2.11 is available ok
OpenMP supported
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c assign.c -o assign.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c between.c -o between.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c bmerge.c -o bmerge.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c chmatch.c -o chmatch.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c cj.c -o cj.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c coalesce.c -o coalesce.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c dogroups.c -o dogroups.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c fastmean.c -o fastmean.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c fcast.c -o fcast.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c fifelse.c -o fifelse.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c fmelt.c -o fmelt.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c forder.c -o forder.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c frank.c -o frank.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c fread.c -o fread.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c freadR.c -o freadR.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c froll.c -o froll.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c frollR.c -o frollR.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c frolladaptive.c -o frolladaptive.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c fsort.c -o fsort.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c fwrite.c -o fwrite.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c fwriteR.c -o fwriteR.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c gsumm.c -o gsumm.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c ijoin.c -o ijoin.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c init.c -o init.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c inrange.c -o inrange.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c nafill.c -o nafill.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c nqrecreateindices.c -o nqrecreateindices.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c openmp-utils.c -o openmp-utils.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c quickselect.c -o quickselect.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c rbindlist.c -o rbindlist.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c reorder.c -o reorder.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c shift.c -o shift.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c snprintf.c -o snprintf.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c subset.c -o subset.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c transpose.c -o transpose.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c types.c -o types.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c uniqlist.c -o uniqlist.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c utils.c -o utils.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c vecseq.c -o vecseq.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2  -fopenmp -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c wrappers.c -o wrappers.o
gcc -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o ijoin.o init.o inrange.o nafill.o nqrecreateindices.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -lz -L/usr/lib64/R/lib -lR
if [ "data.table.so" != "datatable.so" ]; then mv data.table.so datatable.so; fi
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id datatable.so datatable.so; fi
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG  -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG  -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c melt.cpp -o melt.o
g++ -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o reshape2.so RcppExports.o melt.o -L/usr/lib64/R/lib -lR
   checking for file ‘/tmp/RtmpNDokTl/remotes1089c29930afa/SticsRPacks-SticsOnR-c7033ea/DESCRIPTION’ ...
✔  checking for file ‘/tmp/RtmpNDokTl/remotes1089c29930afa/SticsRPacks-SticsOnR-c7033ea/DESCRIPTION’
─  preparing ‘SticsOnR’:
   checking 
   checking DESCRIPTION meta-information ...
✔  checking DESCRIPTION meta-information
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘SticsOnR_0.1.0.9005.tar.gz’
hms        (NA -> 0.5.3) [CRAN]
progress   (NA -> 1.2.2) [CRAN]
cellranger (NA -> 1.1.0) [CRAN]
readxl     (NA -> 1.3.1) [CRAN]
xslt       (NA -> 1.4.2) [CRAN]
lubridate  (NA -> 1.7.9) [CRAN]
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/libxml2 
Using PKG_LIBS=-lexslt -lxslt -lxml2 
rm -f RcppExports.o xslt.o xslt_init.o xslt.so
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -I/usr/include/libxml2  -DSTRICT_R_HEADERS -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/xml2/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -I/usr/include/libxml2  -DSTRICT_R_HEADERS -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/xml2/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c xslt.cpp -o xslt.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -I/usr/include/libxml2  -DSTRICT_R_HEADERS -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/xml2/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c xslt_init.cpp -o xslt_init.o
g++ -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o xslt.so RcppExports.o xslt.o xslt_init.o -lexslt -lxslt -lxml2 -L/usr/lib64/R/lib -lR
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c cctz/src/time_zone_fixed.cc -o cctz/src/time_zone_fixed.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c cctz/src/time_zone_if.cc -o cctz/src/time_zone_if.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c cctz/src/time_zone_impl.cc -o cctz/src/time_zone_impl.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c cctz/src/time_zone_info.cc -o cctz/src/time_zone_info.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c cctz/src/time_zone_libc.cc -o cctz/src/time_zone_libc.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c cctz/src/time_zone_lookup.cc -o cctz/src/time_zone_lookup.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c cctz/src/time_zone_posix.cc -o cctz/src/time_zone_posix.o
ar rcs libcctz.a ./cctz/src/time_zone_fixed.o ./cctz/src/time_zone_if.o ./cctz/src/time_zone_impl.o ./cctz/src/time_zone_info.o ./cctz/src/time_zone_libc.o ./cctz/src/time_zone_lookup.o ./cctz/src/time_zone_posix.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c update.cpp -o update.o
gcc -I"/usr/include/R/" -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c utils.c -o utils.o
gcc -I"/usr/include/R/" -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c datetime.c -o datetime.o
gcc -I"/usr/include/R/" -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c period.c -o period.o
gcc -I"/usr/include/R/" -DNDEBUG -I. -I./cctz/include/ -I./cctz/src/ -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c tparse.c -o tparse.o
g++ -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o lubridate.so RcppExports.o update.o utils.o datetime.o period.o tparse.o -L. -lcctz -L/usr/lib64/R/lib -lR
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -Iunix -I. -DRCPP_DEFAULT_INCLUDE_CALL=false -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/progress/include' -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2  -fvisibility=hidden -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -Iunix -I. -DRCPP_DEFAULT_INCLUDE_CALL=false -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/progress/include' -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2  -fvisibility=hidden -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c XlsWorkBook.cpp -o XlsWorkBook.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -Iunix -I. -DRCPP_DEFAULT_INCLUDE_CALL=false -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/progress/include' -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2  -fvisibility=hidden -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c XlsWorkSheet.cpp -o XlsWorkSheet.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -Iunix -I. -DRCPP_DEFAULT_INCLUDE_CALL=false -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/progress/include' -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2  -fvisibility=hidden -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c XlsxWorkBook.cpp -o XlsxWorkBook.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -Iunix -I. -DRCPP_DEFAULT_INCLUDE_CALL=false -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/progress/include' -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2  -fvisibility=hidden -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c XlsxWorkSheet.cpp -o XlsxWorkSheet.o
gcc -I"/usr/include/R/" -DNDEBUG -Iunix -I. -DRCPP_DEFAULT_INCLUDE_CALL=false -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/progress/include' -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2  -fvisibility=hidden -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c cran.c -o cran.o
gcc -I"/usr/include/R/" -DNDEBUG -Iunix -I. -DRCPP_DEFAULT_INCLUDE_CALL=false -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/progress/include' -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2  -fvisibility=hidden -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c endian.c -o endian.o
gcc -I"/usr/include/R/" -DNDEBUG -Iunix -I. -DRCPP_DEFAULT_INCLUDE_CALL=false -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/progress/include' -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2  -fvisibility=hidden -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c ole.c -o ole.o
gcc -I"/usr/include/R/" -DNDEBUG -Iunix -I. -DRCPP_DEFAULT_INCLUDE_CALL=false -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/progress/include' -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2  -fvisibility=hidden -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c xls.c -o xls.o
gcc -I"/usr/include/R/" -DNDEBUG -Iunix -I. -DRCPP_DEFAULT_INCLUDE_CALL=false -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/progress/include' -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2  -fvisibility=hidden -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c xlstool.c -o xlstool.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -Iunix -I. -DRCPP_DEFAULT_INCLUDE_CALL=false -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/progress/include' -I'/home/drew/.config/ApsimInitiative/ApsimX/rpackages/Rcpp/include' -D_FORTIFY_SOURCE=2  -fvisibility=hidden -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c zip.cpp -o zip.o
g++ -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o readxl.so RcppExports.o XlsWorkBook.o XlsWorkSheet.o XlsxWorkBook.o XlsxWorkSheet.o cran.o endian.o ole.o xls.o xlstool.o zip.o -L/usr/lib64/R/lib -lR
   checking for file ‘/tmp/RtmpNDokTl/remotes1089c79453841/SticsRPacks-SticsRFiles-5408388/DESCRIPTION’ ...
✔  checking for file ‘/tmp/RtmpNDokTl/remotes1089c79453841/SticsRPacks-SticsRFiles-5408388/DESCRIPTION’
─  preparing ‘SticsRFiles’:
   checking DESCRIPTION meta-information ...
✔  checking DESCRIPTION meta-information
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘SticsRFiles_0.1.0.9004.tar.gz’
   checking for file ‘/tmp/RtmpNDokTl/remotes1089c6f4b8ad4/SticsRPacks-SticsRPacks-cf1bd2a/DESCRIPTION’ ...
✔  checking for file ‘/tmp/RtmpNDokTl/remotes1089c6f4b8ad4/SticsRPacks-SticsRPacks-cf1bd2a/DESCRIPTION’
─  preparing ‘SticsRPacks’:
   checking DESCRIPTION meta-information ...
✔  checking DESCRIPTION meta-information
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
   Removed empty directory ‘SticsRPacks/vignettes’
─  building ‘SticsRPacks_0.0.1.9000.tar.gz’

Script contents:
#' Loads a package, installing it if necessary.
#'
#' @param pkg Name of the package to be installed/loaded.
#' @param pkgpath Path where package is to be installed.
#' @return Nothing.
getPackage <- function(pkg, pkgpath) {
    pkgName <- pkg
    if (grepl('/', pkgName, fixed = TRUE)) {
        # if pkg looks like owner/repo, we want pkgName to
        # be just "repo"
        pkgName <- unlist(strsplit(pkgName, '/'))[2]
    }
    if (!pkgName %in% rownames(installed.packages(lib.loc = pkgpath))) {
        if (!dir.exists(pkgpath)) {
            dir.create(pkgpath)
        }
        devtools::install_github(pkg, lib = pkgpath, dependencies = TRUE)
    } else {
        print(paste('Package', pkg, 'is already installed.'))
    }
}

args = commandArgs(TRUE)
getPackage(args[1], args[2])

----------------------------------------------

Context

Please provide any relevant information about your setup. This is important in case the issue is not reproducible except for under certain conditions.

sbuis commented 4 years ago

Hi Drew,

yep, thanks for the report. I fixed the pb (b11ab5f and 17d3631), should work well now. Just note that using dependencies=NA (the default) in install_github should be enough to install all the packages needed to run CroptimizR. Using dependencies=TRUE will install additional packages (those listed in Suggests section of the DESCRIPTION file) that may not be of interest for all your users (e.g. packages related to Stics).

all the best, Samuel

hol430 commented 4 years ago

Ahh, yes the dependencies=TRUE was causing the problem. Thanks for letting me know - and for the quick fix.