Installation broken for R

sreev · May 31, 2019, 3:19am

Following the directions from this link:

fails to install in R.

L-SB8T2T2G3Q-M:apache svaddi$ git clone https://github.com/apache/incubator-mxnet.git
Cloning into 'incubator-mxnet'...
remote: Enumerating objects: 119, done.
remote: Counting objects: 100% (119/119), done.
remote: Compressing objects: 100% (55/55), done.
remote: Total 92684 (delta 85), reused 78 (delta 64), pack-reused 92565
Receiving objects: 100% (92684/92684), 56.96 MiB | 4.09 MiB/s, done.
Resolving deltas: 100% (61481/61481), done.
L-SB8T2T2G3Q-M:apache svaddi$ Rscript -e "install.packages('devtools', repo = 'https://cran.rstudio.com')"
also installing the dependencies ‘ini’, ‘desc’, ‘rprojroot’, ‘xopen’, ‘clisymbols’, ‘gh’, ‘git2r’, ‘memoise’, ‘pkgbuild’, ‘pkgload’, ‘rcmdcheck’, ‘remotes’, ‘sessioninfo’, ‘usethis’

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/ini_0.3.1.tgz'
Content type 'application/x-gzip' length 13465 bytes (13 KB)
==================================================
downloaded 13 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/desc_1.2.0.tgz'
Content type 'application/x-gzip' length 288062 bytes (281 KB)
==================================================
downloaded 281 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/rprojroot_1.3-2.tgz'
Content type 'application/x-gzip' length 79547 bytes (77 KB)
==================================================
downloaded 77 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/xopen_1.0.0.tgz'
Content type 'application/x-gzip' length 22742 bytes (22 KB)
==================================================
downloaded 22 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/clisymbols_1.2.0.tgz'
Content type 'application/x-gzip' length 18007 bytes (17 KB)
==================================================
downloaded 17 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/gh_1.0.1.tgz'
Content type 'application/x-gzip' length 48411 bytes (47 KB)
==================================================
downloaded 47 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/git2r_0.25.2.tgz'
Content type 'application/x-gzip' length 2059943 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/memoise_1.1.0.tgz'
Content type 'application/x-gzip' length 35030 bytes (34 KB)
==================================================
downloaded 34 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/pkgbuild_1.0.3.tgz'
Content type 'application/x-gzip' length 133329 bytes (130 KB)
==================================================
downloaded 130 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/pkgload_1.0.2.tgz'
Content type 'application/x-gzip' length 147177 bytes (143 KB)
==================================================
downloaded 143 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/rcmdcheck_1.3.3.tgz'
Content type 'application/x-gzip' length 132445 bytes (129 KB)
==================================================
downloaded 129 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/remotes_2.0.4.tgz'
Content type 'application/x-gzip' length 317843 bytes (310 KB)
==================================================
downloaded 310 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/sessioninfo_1.1.1.tgz'
Content type 'application/x-gzip' length 44783 bytes (43 KB)
==================================================
downloaded 43 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/usethis_1.5.0.tgz'
Content type 'application/x-gzip' length 684992 bytes (668 KB)
==================================================
downloaded 668 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/devtools_2.0.2.tgz'
Content type 'application/x-gzip' length 385123 bytes (376 KB)
==================================================
downloaded 376 KB


The downloaded binary packages are in
	/var/folders/40/_cbf9y0936x52h1fk8tlvrlm0000gn/T//RtmpUj6kXy/downloaded_packages

L-SB8T2T2G3Q-M:apache svaddi$ cd incubator-mxnet/

L-SB8T2T2G3Q-M:incubator-mxnet svaddi$ cd R-package/

L-SB8T2T2G3Q-M:R-package svaddi$ Rscript -e "library(devtools); library(methods); options(repos=c(CRAN='https://cran.rstudio.com')); install_deps(dependencies = TRUE)
> "
bmp        (NA    -> 0.3   ) [CRAN]
Cairo      (NA    -> 1.5-10) [CRAN]
covr       (NA    -> 3.2.1 ) [CRAN]
evaluate   (0.13  -> 0.14  ) [CRAN]
imager     (NA    -> 0.41.2) [CRAN]
jpeg       (NA    -> 0.1-8 ) [CRAN]
mlbench    (NA    -> 2.1-1 ) [CRAN]
pillar     (1.4.0 -> 1.4.1 ) [CRAN]
png        (NA    -> 0.1-7 ) [CRAN]
praise     (NA    -> 1.0.0 ) [CRAN]
readbitmap (NA    -> 0.1.5 ) [CRAN]
rex        (NA    -> 1.1.2 ) [CRAN]
testthat   (NA    -> 2.1.1 ) [CRAN]
tibble     (2.1.1 -> 2.1.2 ) [CRAN]
tiff       (NA    -> 0.1-5 ) [CRAN]
Installing 15 packages: bmp, Cairo, covr, evaluate, imager, jpeg, mlbench, pillar, png, praise, readbitmap, rex, testthat, tibble, tiff
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/bmp_0.3.tgz'
Content type 'application/x-gzip' length 122452 bytes (119 KB)
==================================================
downloaded 119 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/Cairo_1.5-10.tgz'
Content type 'application/x-gzip' length 299981 bytes (292 KB)
==================================================
downloaded 292 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/covr_3.2.1.tgz'
Content type 'application/x-gzip' length 276046 bytes (269 KB)
==================================================
downloaded 269 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/evaluate_0.14.tgz'
Content type 'application/x-gzip' length 74657 bytes (72 KB)
==================================================
downloaded 72 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/imager_0.41.2.tgz'
Content type 'application/x-gzip' length 12238693 bytes (11.7 MB)
==================================================
downloaded 11.7 MB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/jpeg_0.1-8.tgz'
Content type 'application/x-gzip' length 389601 bytes (380 KB)
==================================================
downloaded 380 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/mlbench_2.1-1.tgz'
Content type 'application/x-gzip' length 1049675 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/pillar_1.4.1.tgz'
Content type 'application/x-gzip' length 177160 bytes (173 KB)
==================================================
downloaded 173 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/png_0.1-7.tgz'
Content type 'application/x-gzip' length 354111 bytes (345 KB)
==================================================
downloaded 345 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/praise_1.0.0.tgz'
Content type 'application/x-gzip' length 16379 bytes (15 KB)
==================================================
downloaded 15 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/readbitmap_0.1.5.tgz'
Content type 'application/x-gzip' length 17074 bytes (16 KB)
==================================================
downloaded 16 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/rex_1.1.2.tgz'
Content type 'application/x-gzip' length 120784 bytes (117 KB)
==================================================
downloaded 117 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/testthat_2.1.1.tgz'
Content type 'application/x-gzip' length 2325331 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/tibble_2.1.2.tgz'
Content type 'application/x-gzip' length 318118 bytes (310 KB)
==================================================
downloaded 310 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/tiff_0.1-5.tgz'
Content type 'application/x-gzip' length 852120 bytes (832 KB)
==================================================
downloaded 832 KB


The downloaded binary packages are in
	/var/folders/40/_cbf9y0936x52h1fk8tlvrlm0000gn/T//RtmpPPTT9K/downloaded_packages

L-SB8T2T2G3Q-M:R-package svaddi$ cd ..

L-SB8T2T2G3Q-M:incubator-mxnet svaddi$ make rpkg
Makefile:83: /Users/svaddi/SreeVaddi/source/github/apache/incubator-mxnet/3rdparty/mshadow/make/mshadow.mk: No such file or directory
Makefile:84: /Users/svaddi/SreeVaddi/source/github/apache/incubator-mxnet/3rdparty/dmlc-core/make/dmlc.mk: No such file or directory
Makefile:345: WARNING: Significant performance increases can be achieved by installing and enabling gperftools or jemalloc development packages
Makefile:416: /Users/svaddi/SreeVaddi/source/github/apache/incubator-mxnet/3rdparty/ps-lite/make/ps.mk: No such file or directory
make: *** No rule to make target `/Users/svaddi/SreeVaddi/source/github/apache/incubator-mxnet/3rdparty/ps-lite/make/ps.mk'.  Stop.

sreev · May 31, 2019, 5:37am

> install.packages("https://s3.ca-central-1.amazonaws.com/jeremiedb/share/mxnet/CPU/3.6/mxnet.zip", repos = NULL, type="source")
trying URL 'https://s3.ca-central-1.amazonaws.com/jeremiedb/share/mxnet/CPU/3.6/mxnet.zip'
Content type 'application/zip' length 31543727 bytes (30.1 MB)
==================================================
downloaded 30.1 MB

Error in rawToChar(block[seq_len(ns)]) : 
  embedded nul in string: 'PK\003\004\024\0\0\0\0\0\xa2\xa0\xa8N\0\0\0\0\0\0\0\0\0\0\0\0\006\0\0\0mxnet/PK\003\004\024\0\0\0\0\0r\xa0\xa8N\0\0\0\0\0\0\0\0\0\0\0\0\v\0\0\0mxnet/demo/PK\003\004\024\0\0\0\b\0r\xa0\xa8N\x85\xe1\xa2\rQ\002\0\0\037'
Warning in install.packages :
  installation of package ‘/var/folders/40/_cbf9y0936x52h1fk8tlvrlm0000gn/T//Rtmp7l3sMe/downloaded_packages/mxnet.zip’ had non-zero exit status

sreev · May 31, 2019, 5:37am

> library(devtools)
> install_github("apache/incubator-mxnet/R-package")
Downloading GitHub repo apache/incubator-mxnet@master
Error: Does not appear to be an R package (no DESCRIPTION)

sreev · May 31, 2019, 5:38am

> library(devtools)
> install.packages("/Users/svaddi/Downloads/apache-mxnet-src-1.4.1-incubating.tar.gz", repos=NULL, type="source")
ERROR: cannot extract package from ‘/Users/svaddi/Downloads/apache-mxnet-src-1.4.1-incubating.tar.gz’
Warning message:
In install.packages("/Users/svaddi/Downloads/apache-mxnet-src-1.4.1-incubating.tar.gz",  :
  installation of package ‘/Users/svaddi/Downloads/apache-mxnet-src-1.4.1-incubating.tar.gz’ had non-zero exit status

Aaron_Markham · June 5, 2019, 4:26pm

Downgrade R to 3.5.x then try again. I updated the instructions recently to reflect this requirement.

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Installation broken for R

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