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Errors in installing sake pacakge #70

Closed Yoon-Seob-Kim closed 6 years ago

Yoon-Seob-Kim commented 6 years ago

Hello

I have difficulty in installing sake pacakge

The below is the console of my R studio.

How can I do to fix the error?

Thanks for your help...

Downloading GitHub repo naikai/sake@master from URL https://api.github.com/repos/naikai/sake/zipball/master Installing sake Downloading GitHub repo renozao/NMF@master from URL https://api.github.com/repos/renozao/NMF/zipball/master Installing NMF --2018-04-26 12:37:02-- https://cran.rstudio.com/src/contrib/dendextend_1.7.0.tar.gz Resolving cran.rstudio.com (cran.rstudio.com)... 52.84.188.72 Connecting to cran.rstudio.com (cran.rstudio.com)|52.84.188.72|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1747651 (1.7M) [application/x-gzip] Saving to: ‘/tmp/RtmpYmGag2/dendextend_1.7.0.tar.gz’ 0K .......... .......... .......... .......... .......... 2% 7.94M 0s 50K .......... .......... .......... .......... .......... 5% 11.9M 0s 100K .......... .......... .......... .......... .......... 8% 11.6M 0s 150K .......... .......... .......... .......... .......... 11% 11.5M 0s 200K .......... .......... .......... .......... .......... 14% 11.5M 0s 250K .......... .......... .......... .......... .......... 17% 11.6M 0s 300K .......... .......... .......... .......... .......... 20% 11.6M 0s 350K .......... .......... .......... .......... .......... 23% 8.86M 0s 400K .......... .......... .......... .......... .......... 26% 11.7M 0s 450K .......... .......... .......... .......... .......... 29% 11.6M 0s 500K .......... .......... .......... .......... .......... 32% 11.8M 0s 550K .......... .......... .......... .......... .......... 35% 11.6M 0s 600K .......... .......... .......... .......... .......... 38% 11.7M 0s 650K .......... .......... .......... .......... .......... 41% 11.7M 0s 700K .......... .......... .......... .......... .......... 43% 11.8M 0s 750K .......... .......... .......... .......... .......... 46% 8.85M 0s 800K .......... .......... .......... .......... .......... 49% 11.6M 0s 850K .......... .......... .......... .......... .......... 52% 11.7M 0s 900K .......... .......... .......... .......... .......... 55% 11.7M 0s 950K .......... .......... .......... .......... .......... 58% 11.5M 0s 1000K .......... .......... .......... .......... .......... 61% 11.7M 0s 1050K .......... .......... .......... .......... .......... 64% 11.6M 0s 1100K .......... .......... .......... .......... .......... 67% 11.6M 0s 1150K .......... .......... .......... .......... .......... 70% 8.88M 0s 1200K .......... .......... .......... .......... .......... 73% 11.6M 0s 1250K .......... .......... .......... .......... .......... 76% 11.7M 0s 1300K .......... .......... .......... .......... .......... 79% 11.7M 0s 1350K .......... .......... .......... .......... .......... 82% 11.6M 0s 1400K .......... .......... .......... .......... .......... 84% 11.7M 0s 1450K .......... .......... .......... .......... .......... 87% 11.6M 0s 1500K .......... .......... .......... .......... .......... 90% 11.7M 0s 1550K .......... .......... .......... .......... .......... 93% 8.63M 0s 1600K .......... .......... .......... .......... .......... 96% 11.6M 0s 1650K .......... .......... .......... .......... .......... 99% 13.2M 0s 1700K ...... 100% 349M=0.1s 2018-04-26 12:37:02 (11.2 MB/s) - ‘/tmp/RtmpYmGag2/dendextend_1.7.0.tar.gz’ saved [1747651/1747651] Installing dendextend --2018-04-26 12:37:04-- https://cran.rstudio.com/src/contrib/fpc_2.1-11.tar.gz Resolving cran.rstudio.com (cran.rstudio.com)... 52.84.188.72 Connecting to cran.rstudio.com (cran.rstudio.com)|52.84.188.72|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 152399 (149K) [application/x-gzip] Saving to: ‘/tmp/RtmpYmGag2/fpc_2.1-11.tar.gz’ 0K .......... .......... .......... .......... .......... 33% 5.20M 0s 50K .......... .......... .......... .......... .......... 67% 11.6M 0s 100K .......... .......... .......... .......... ........ 100% 14.9M=0.02s 2018-04-26 12:37:04 (8.66 MB/s) - ‘/tmp/RtmpYmGag2/fpc_2.1-11.tar.gz’ saved [152399/152399] Installing fpc --2018-04-26 12:37:05-- https://cran.rstudio.com/src/contrib/flexmix_2.3-14.tar.gz Resolving cran.rstudio.com (cran.rstudio.com)... 52.84.188.72 Connecting to cran.rstudio.com (cran.rstudio.com)|52.84.188.72|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1169493 (1.1M) [application/x-gzip] Saving to: ‘/tmp/RtmpYmGag2/flexmix_2.3-14.tar.gz’ 0K .......... .......... .......... .......... .......... 4% 8.02M 0s 50K .......... .......... .......... .......... .......... 8% 11.6M 0s 100K .......... .......... .......... .......... .......... 13% 11.7M 0s 150K .......... .......... .......... .......... .......... 17% 11.6M 0s 200K .......... .......... .......... .......... .......... 21% 11.7M 0s 250K .......... .......... .......... .......... .......... 26% 11.6M 0s 300K .......... .......... .......... .......... .......... 30% 11.7M 0s 350K .......... .......... .......... .......... .......... 35% 8.89M 0s 400K .......... .......... .......... .......... .......... 39% 11.7M 0s 450K .......... .......... .......... .......... .......... 43% 11.7M 0s 500K .......... .......... .......... .......... .......... 48% 11.7M 0s 550K .......... .......... .......... .......... .......... 52% 11.6M 0s 600K .......... .......... .......... .......... .......... 56% 11.7M 0s 650K .......... .......... .......... .......... .......... 61% 11.5M 0s 700K .......... .......... .......... .......... .......... 65% 10.3M 0s 750K .......... .......... .......... .......... .......... 70% 11.2M 0s 800K .......... .......... .......... .......... .......... 74% 11.8M 0s 850K .......... .......... .......... .......... .......... 78% 9.45M 0s 900K .......... .......... .......... .......... .......... 83% 14.6M 0s 950K .......... .......... .......... .......... .......... 87% 9.07M 0s 1000K .......... .......... .......... .......... .......... 91% 11.6M 0s 1050K .......... .......... .......... .......... .......... 96% 11.6M 0s 1100K .......... .......... .......... .......... .. 100% 15.2M=0.1s 2018-04-26 12:37:06 (11.1 MB/s) - ‘/tmp/RtmpYmGag2/flexmix_2.3-14.tar.gz’ saved [1169493/1169493] Installing flexmix '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/tmp/RtmpYmGag2/devtools4376222579c0/flexmix' --library='/home/kys/R/x86_64-pc-linux-gnu-library/3.2' --install-tests * installing *source* package ‘flexmix’ ... ** package ‘flexmix’ successfully unpacked and MD5 sums checked ** R ** data ** inst ** preparing package for lazy loading Error in loadNamespace(name) : there is no package called ‘lme4’ Error : unable to load R code in package ‘flexmix’ ERROR: lazy loading failed for package ‘flexmix’ * removing ‘/home/kys/R/x86_64-pc-linux-gnu-library/3.2/flexmix’ Installation failed: Command failed (1) '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/tmp/RtmpYmGag2/devtools4376360db227/fpc' --library='/home/kys/R/x86_64-pc-linux-gnu-library/3.2' --install-tests ERROR: dependency ‘flexmix’ is not available for package ‘fpc’ * removing ‘/home/kys/R/x86_64-pc-linux-gnu-library/3.2/fpc’ Installation failed: Command failed (1) '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/tmp/RtmpYmGag2/devtools43767b2a2854/dendextend' --library='/home/kys/R/x86_64-pc-linux-gnu-library/3.2' --install-tests ERROR: dependency ‘fpc’ is not available for package ‘dendextend’ * removing ‘/home/kys/R/x86_64-pc-linux-gnu-library/3.2/dendextend’ Installation failed: Command failed (1) '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/tmp/RtmpYmGag2/devtools43765e48c1a8/renozao-NMF-e46bec1' --library='/home/kys/R/x86_64-pc-linux-gnu-library/3.2' \ --install-tests ERROR: dependency ‘dendextend’ is not available for package ‘NMF’ * removing ‘/home/kys/R/x86_64-pc-linux-gnu-library/3.2/NMF’ Installation failed: Command failed (1) Downloading GitHub repo rstudio/d3heatmap@colorlabels from URL https://api.github.com/repos/rstudio/d3heatmap/zipball/colorlabels Installing d3heatmap --2018-04-26 12:37:10-- https://cran.rstudio.com/src/contrib/dendextend_1.7.0.tar.gz Resolving cran.rstudio.com (cran.rstudio.com)... 52.84.188.72 Connecting to cran.rstudio.com (cran.rstudio.com)|52.84.188.72|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1747651 (1.7M) [application/x-gzip] Saving to: ‘/tmp/RtmpYmGag2/dendextend_1.7.0.tar.gz’ 0K .......... .......... .......... .......... .......... 2% 7.65M 0s 50K .......... .......... .......... .......... .......... 5% 11.7M 0s 100K .......... .......... .......... .......... .......... 8% 11.7M 0s 150K .......... .......... .......... .......... .......... 11% 11.6M 0s 200K .......... .......... .......... .......... .......... 14% 11.7M 0s 250K .......... .......... .......... .......... .......... 17% 9.13M 0s 300K .......... .......... .......... .......... .......... 20% 8.82M 0s 350K .......... .......... .......... .......... .......... 23% 8.18M 0s 400K .......... .......... .......... .......... .......... 26% 11.6M 0s 450K .......... .......... .......... .......... .......... 29% 11.7M 0s 500K .......... .......... .......... .......... .......... 32% 11.7M 0s 550K .......... .......... .......... .......... .......... 35% 11.4M 0s 600K .......... .......... .......... .......... .......... 38% 8.23M 0s 650K .......... .......... .......... .......... .......... 41% 9.27M 0s 700K .......... .......... .......... .......... .......... 43% 11.4M 0s 750K .......... .......... .......... .......... .......... 46% 9.11M 0s 800K .......... .......... .......... .......... .......... 49% 11.7M 0s 850K .......... .......... .......... .......... .......... 52% 11.6M 0s 900K .......... .......... .......... .......... .......... 55% 11.7M 0s 950K .......... .......... .......... .......... .......... 58% 11.6M 0s 1000K .......... .......... .......... .......... .......... 61% 11.4M 0s 1050K .......... .......... .......... .......... .......... 64% 11.7M 0s 1100K .......... .......... .......... .......... .......... 67% 11.6M 0s 1150K .......... .......... .......... .......... .......... 70% 8.86M 0s 1200K .......... .......... .......... .......... .......... 73% 11.7M 0s 1250K .......... .......... .......... .......... .......... 76% 11.7M 0s 1300K .......... .......... .......... .......... .......... 79% 11.6M 0s 1350K .......... .......... .......... .......... .......... 82% 11.6M 0s 1400K .......... .......... .......... .......... .......... 84% 11.7M 0s 1450K .......... .......... .......... .......... .......... 87% 11.6M 0s 1500K .......... .......... .......... .......... .......... 90% 7.99M 0s 1550K .......... .......... .......... .......... .......... 93% 7.36M 0s 1600K .......... .......... .......... .......... .......... 96% 8.03M 0s 1650K .......... .......... .......... .......... .......... 99% 8.53M 0s 1700K ...... 100% 390M=0.2s 2018-04-26 12:37:10 (10.3 MB/s) - ‘/tmp/RtmpYmGag2/dendextend_1.7.0.tar.gz’ saved [1747651/1747651] Skipping dendextend, it is already being installed. '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/tmp/RtmpYmGag2/devtools437634e4343f/rstudio-d3heatmap-5685d6a' --library='/home/kys/R/x86_64-pc-linux-gnu-library/3.2' \ --install-tests ERROR: dependency ‘dendextend’ is not available for package ‘d3heatmap’ * removing ‘/home/kys/R/x86_64-pc-linux-gnu-library/3.2/d3heatmap’ Installation failed: Command failed (1) '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/tmp/RtmpYmGag2/devtools43767151571a/naikai-sake-ab95930' --library='/home/kys/R/x86_64-pc-linux-gnu-library/3.2' \ --install-tests ERROR: dependencies ‘NMF’, ‘d3heatmap’ are not available for package ‘sake’ * removing ‘/home/kys/R/x86_64-pc-linux-gnu-library/3.2/sake’ Installation failed: Command failed (1)
molikd commented 6 years ago

For clarification, what operating system are you running?

This output shows that you are failing to locate the lme4 package. The first thing I would try is to try to install this package: install.packages("lme4")

Yoon-Seob-Kim commented 6 years ago

install.packages("lme4") did not work due to same dependency issue my OS is ubuntu 16.04 Desktop LTS (64-bit) Thanks.

molikd commented 6 years ago

have you installed the ubuntu dependencies: sudo apt-get install libcurl4-openssl-dev libpng-dev libxslt-dev libssl-dev libxml2-dev xsltproc

you can also try installing lme4 via github: install_github("lme4/lme4",dependencies=TRUE)

Yoon-Seob-Kim commented 6 years ago

I already installed the ubuntu dependencies...

But fortunately I fixed the problem

I suspect the OS problem, and I tried to install ubuntu 18 ver via virtualbox machine on win 10 system.

And then ... it worked!! thanks for your kind help