Streamlit app running locally but doesn't work when published - streamlit

I am trying to run an app on Streamlit, I've tested it successfully locally and everything works but when I initialize it on streamlit it installs dependencies and then stops without any appropriate errors.
This is the error log and it pulls everything from my github repository.
the app essentially takes a phrase and paraphrases it through Parrot and then uses GPT Neo to generate an article and writes it to the app
[     UTC     ] Logs for student1043-articlescraper-streamlitfilter-pwqkhs.streamlitapp.com/
────────────────────────────────────────────────────────────────────────────────────────
[17:20:06] 🚀 Starting up repository: 'articlescraper', branch: 'main', main module: 'streamlitfilter.py'
[17:20:06] 🐙 Cloning repository...
[17:20:07] 🐙 Cloning into '/app/articlescraper'...
[17:20:07] 🐙 Cloned repository!
[17:20:07] 🐙 Pulling code changes from Github...
[17:20:08] 📦 Processing dependencies...
──────────────────────────────────────── pip ───────────────────────────────────────────
Collecting git+https://github.com/PrithivirajDamodaran/Parrot_Paraphraser.git (from -r /app/articlescraper/requirements.txt (line 6))
Cloning https://github.com/PrithivirajDamodaran/Parrot_Paraphraser.git to /tmp/pip-req-build-t7d0azd1
Running command git clone --filter=blob:none --quiet https://github.com/PrithivirajDamodaran/Parrot_Paraphraser.git /tmp/pip-req-build-t7d0azd1
Resolved https://github.com/PrithivirajDamodaran/Parrot_Paraphraser.git to commit 3bc88f0efde65da558a1e6b2b6625761e0fba3c4
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting transformers
Downloading transformers-4.20.1-py3-none-any.whl (4.4 MB)
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Collecting sentencepiece
Downloading sentencepiece-0.1.96-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.2 MB)
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Collecting python-Levenshtein
Downloading python-Levenshtein-0.12.2.tar.gz (50 kB)
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Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting fuzzywuzzy
Downloading fuzzywuzzy-0.18.0-py2.py3-none-any.whl (18 kB)
Collecting sentence-transformers
Downloading sentence-transformers-2.2.2.tar.gz (85 kB)
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Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting torch
Downloading torch-1.12.0-cp37-cp37m-manylinux1_x86_64.whl (776.3 MB)
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Collecting filelock
Downloading filelock-3.7.1-py3-none-any.whl (10 kB)
Collecting importlib-metadata
Downloading importlib_metadata-4.12.0-py3-none-any.whl (21 kB)
Collecting pyyaml>=5.1
Downloading PyYAML-6.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (596 kB)
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Collecting numpy>=1.17
Downloading numpy-1.21.6-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
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Collecting tokenizers!=0.11.3,<0.13,>=0.11.1
Downloading tokenizers-0.12.1-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (6.6 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.6/6.6 MB 190.4 MB/s eta 0:00:00[2022-07-17 17:20:25.737717]
Collecting requests
Downloading requests-2.28.1-py3-none-any.whl (62 kB)
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Collecting packaging>=20.0
Downloading packaging-21.3-py3-none-any.whl (40 kB)
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Collecting huggingface-hub<1.0,>=0.1.0
Downloading huggingface_hub-0.8.1-py3-none-any.whl (101 kB)
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Collecting regex!=2019.12.17
Downloading regex-2022.7.9-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (749 kB)
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Collecting tqdm>=4.27
Downloading tqdm-4.64.0-py2.py3-none-any.whl (78 kB)
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Collecting setuptools
Downloading setuptools-63.2.0-py3-none-any.whl (1.2 MB)
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Collecting torchvision
Downloading torchvision-0.13.0-cp37-cp37m-manylinux1_x86_64.whl (19.1 MB)
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Collecting scikit-learn
Downloading scikit_learn-1.0.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (24.8 MB)
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Collecting scipy
Downloading scipy-1.7.3-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (38.1 MB)
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Collecting nltk
Downloading nltk-3.7-py3-none-any.whl (1.5 MB)
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Collecting typing-extensions
Downloading typing_extensions-4.3.0-py3-none-any.whl (25 kB)
Collecting pyparsing!=3.0.5,>=2.0.2
Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB)
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Collecting zipp>=0.5
Downloading zipp-3.8.1-py3-none-any.whl (5.6 kB)
Collecting joblib
Downloading joblib-1.1.0-py2.py3-none-any.whl (306 kB)
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Collecting click
Downloading click-8.1.3-py3-none-any.whl (96 kB)
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Collecting urllib3<1.27,>=1.21.1
Downloading urllib3-1.26.10-py2.py3-none-any.whl (139 kB)
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Collecting charset-normalizer<3,>=2
Downloading charset_normalizer-2.1.0-py3-none-any.whl (39 kB)
Collecting certifi>=2017.4.17
Downloading certifi-2022.6.15-py3-none-any.whl (160 kB)
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Collecting idna<4,>=2.5
Downloading idna-3.3-py3-none-any.whl (61 kB)
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Collecting threadpoolctl>=2.0.0
Downloading threadpoolctl-3.1.0-py3-none-any.whl (14 kB)
Collecting pillow!=8.3.*,>=5.3.0
Downloading Pillow-9.2.0-cp37-cp37m-manylinux_2_28_x86_64.whl (3.2 MB)
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Building wheels for collected packages: python-Levenshtein, sentence-transformers, parrot
Building wheel for python-Levenshtein (setup.py): started
Building wheel for python-Levenshtein (setup.py): finished with status 'done'
Created wheel for python-Levenshtein: filename=python_Levenshtein-0.12.2-cp37-cp37m-linux_x86_64.whl size=83198 sha256=d7aa6d954ef7912f5666162d9cbeba4148d79fe6e0a839a8799e2205c43c29e8
Stored in directory: /tmp/pip-ephem-wheel-cache-kbhfw62r/wheels/05/5f/ca/7c4367734892581bb5ff896f15027a932c551080b2abd3e00d
Building wheel for sentence-transformers (setup.py): started
Building wheel for sentence-transformers (setup.py): finished with status 'done'
Created wheel for sentence-transformers: filename=sentence_transformers-2.2.2-py3-none-any.whl size=125925 sha256=8661061ec046df6147c4c771c95cd01ebeb2760ca6518ff0877daf89d3380848
Stored in directory: /tmp/pip-ephem-wheel-cache-kbhfw62r/wheels/bf/06/fb/d59c1e5bd1dac7f6cf61ec0036cc3a10ab8fecaa6b2c3d3ee9
Building wheel for parrot (setup.py): started
Building wheel for parrot (setup.py): finished with status 'done'
Created wheel for parrot: filename=parrot-1.0-py3-none-any.whl size=8583 sha256=fcdff33a813d7cd2a86980dc66127ef5abb71fac9d5b89fde83e92bb41c070f4
Stored in directory: /tmp/pip-ephem-wheel-cache-kbhfw62r/wheels/ff/27/79/a53e92f32da44c8c4f51094ca156e6ff91103b7e48a341d62b
Successfully built python-Levenshtein sentence-transformers parrot
Installing collected packages: tokenizers, sentencepiece, fuzzywuzzy, zipp, urllib3, typing-extensions, tqdm, threadpoolctl, setuptools, regex, pyyaml, pyparsing, pillow, numpy, joblib, idna, filelock, charset-normalizer, certifi, torch, scipy, requests, python-Levenshtein, packaging, importlib-metadata, torchvision, scikit-learn, huggingface-hub, click, transformers, nltk, sentence-transformers, parrot
Attempting uninstall: setuptools
Found existing installation: setuptools 62.6.0
Uninstalling setuptools-62.6.0:
Successfully uninstalled setuptools-62.6.0
[17:21:14] 🖥 Provisioning machine...
Successfully installed certifi-2022.6.15 charset-normalizer-2.1.0 click-8.1.3 filelock-3.7.1 fuzzywuzzy-0.18.0 huggingface-hub-0.8.1 idna-3.3 importlib-metadata-4.12.0 joblib-1.1.0 nltk-3.7 numpy-1.21.6 packaging-21.3 parrot-1.0 pillow-9.2.0 pyparsing-3.0.9 python-Levenshtein-0.12.2 pyyaml-6.0 regex-2022.7.9 requests-2.28.1 scikit-learn-1.0.2 scipy-1.7.3 sentence-transformers-2.2.2 sentencepiece-0.1.96 setuptools-63.2.0 threadpoolctl-3.1.0 tokenizers-0.12.1 torch-1.12.0 torchvision-0.13.0 tqdm-4.64.0 transformers-4.20.1 typing-extensions-4.3.0 urllib3-1.26.10 zipp-3.8.1
WARNING: You are using pip version 22.0.3; however, version 22.1.2 is available.
You should consider upgrading via the '/home/appuser/venv/bin/python -m pip install --upgrade pip' command.
Checking if Streamlit is installed
────────────────────────────────────────────────────────────────────────────────────────
[17:21:21] 🎛 Preparing system...
[17:21:21] ⛓ Spinning up manager process...
[17:21:21] 🐍 Python dependencies were installed from /app/articlescraper/requirements.txt using pip.
Check if streamlit is installed

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downloaded 15.8 MB
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Content type 'application/zip' length 878540 bytes (857 KB)
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downloaded 857 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/DBI_1.1.0.zip'
Content type 'application/zip' length 656596 bytes (641 KB)
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Content type 'application/zip' length 1223853 bytes (1.2 MB)
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Content type 'application/zip' length 157428 bytes (153 KB)
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downloaded 153 KB
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==================================================
downloaded 3.8 MB
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.3.zip'
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downloaded 1.1 MB
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Content type 'application/zip' length 1749669 bytes (1.7 MB)
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downloaded 54 KB
package 'RGtk2' successfully unpacked and MD5 sums checked
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problem copying C:\Users\vanvj\Documents\R\R-4.0.0\library\00LOCK\RGtk2\gtk\x64\bin\libatk-1.0-0.dll to C:\Users\vanvj\Documents\R\R-4.0.0\library\RGtk2\gtk\x64\bin\libatk-1.0-0.dll: Permission denied
Warning in file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\vanvj\Documents\R\R-4.0.0\library\00LOCK\RGtk2\libs\x64\RGtk2.dll to C:\Users\vanvj\Documents\R\R-4.0.0\library\RGtk2\libs\x64\RGtk2.dll: Permission denied
Warning: restored 'RGtk2'
package 'RODBC' successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package 'RODBC'
Warning in file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\vanvj\Documents\R\R-4.0.0\library\00LOCK\RODBC\libs\x64\RODBC.dll to C:\Users\vanvj\Documents\R\R-4.0.0\library\RODBC\libs\x64\RODBC.dll: Permission denied
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package 'DBI' successfully unpacked and MD5 sums checked
package 'sqldf' successfully unpacked and MD5 sums checked
package 'FSA' successfully unpacked and MD5 sums checked
package 'magrittr' successfully unpacked and MD5 sums checked
package 'dplyr' successfully unpacked and MD5 sums checked
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package 'ggplot2' successfully unpacked and MD5 sums checked
package 'gridExtra' successfully unpacked and MD5 sums checked
package 'lubridate' successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package 'lubridate'
Warning in file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\vanvj\Documents\R\R-4.0.0\library\00LOCK\lubridate\libs\x64\lubridate.dll to C:\Users\vanvj\Documents\R\R-4.0.0\library\lubridate\libs\x64\lubridate.dll: Permission denied
Warning: restored 'lubridate'
package 'devtools' successfully unpacked and MD5 sums checked
package 'roxygen2' successfully unpacked and MD5 sums checked
package 'RColorBrewer' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\vanvj\AppData\Local\Temp\10\Rtmpm2yhXI\downloaded_packages
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/RColorBrewer_1.1-2.zip'
Content type 'application/zip' length 55583 bytes (54 KB)
==================================================
downloaded 54 KB
|
package 'RColorBrewer' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\vanvj\AppData\Local\Temp\10\Rtmpm2yhXI\downloaded_packages
Error : Can't find 'C:\Users\VANVES~1\AppData\Local\Temp\10\RtmpSseu9k\R.INSTALL1a085e0947fd\Radamas\ABioQuery'.
Error: unable to load R code in package 'Radamas'
Execution halted
Error in (function (command = NULL, args = character(), error_on_status = TRUE, :
System command 'Rcmd.exe' failed, exit status: 1, stdout & stderr were printed
Type .Last.error.trace to see where the error occured
> .Last.error.trace
Stack trace:
1. devtools:::install("Radamas")
2. pkgbuild::with_build_tools(required = FALSE, callr::rcmd("INSTALL", ...
3. withr::with_path(rtools_path(), code)
4. base:::force(code)
5. callr::rcmd("INSTALL", c(install_path, opts), echo = !quiet, ...
6. callr:::run_r(options)
7. base:::with(options, with_envvar(env, do.call(processx::run, ...
8. base:::with.default(options, with_envvar(env, do.call(processx::run, ...
9. base:::eval(substitute(expr), data, enclos = parent.frame())
10. base:::eval(substitute(expr), data, enclos = parent.frame())
11. callr:::with_envvar(env, do.call(processx::run, c(list(bin, args = real_cmdargs, ...
12. base:::force(code)
13. base:::do.call(processx::run, c(list(bin, args = real_cmdargs, ...
14. (function (command = NULL, args = character(), error_on_status = TRUE, ...
15. throw(new_process_error(res, call = sys.call(), echo = echo, ...
x System command 'Rcmd.exe' failed, exit status: 1, stdout & stderr were printed
Could anyone at least point me in the direction of how to address this error? I admittedly don't even know what the errors are telling me, even after days of google searches. Thank you!
Well, the binary package is reported to be in
C:\Users\ vanvj \AppData\Local\Temp\10\Rtmpm2yhXI\downloaded_packages
and then the error message says it was looking in
Can't find 'C:\Users\ VANVES~1 \AppData\Local\Temp\10\RtmpSseu9k\R.INSTALL1a085e0947fd\Radamas\ABioQuery'.
That suggests that the originator of the package may have hard-coded his username into something in the build code. I'm not 100$ sure, but I'd start by looking in your appdata\local\temp\10... directories and see what you find.

Can't install packages in RStudio - blocked after download

I'm trying to install the package "sqldf" in RStudio but it blocks after downloading few packages
R version 3.5.0 (2018-04-23)
> install.packages("sqldf")
Installing package into ‘C:/Users/sperga/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
also installing the dependencies ‘BH’, ‘plogr’, ‘gsubfn’, ‘proto’, ‘RSQLite’, ‘DBI’, ‘chron’
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/BH_1.66.0-1.zip'
Content type 'application/zip' length 17880019 bytes (17.1 MB)
downloaded 17.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/plogr_0.2.0.zip'
Content type 'application/zip' length 18718 bytes (18 KB)
downloaded 18 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/gsubfn_0.7.zip'
Content type 'application/zip' length 357663 bytes (349 KB)
downloaded 349 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/proto_1.0.0.zip'
Content type 'application/zip' length 471954 bytes (460 KB)
downloaded 460 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/RSQLite_2.1.1.zip'
Content type 'application/zip' length 2154846 bytes (2.1 MB)
downloaded 2.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/DBI_1.0.0.zip'
Content type 'application/zip' length 887210 bytes (866 KB)
downloaded 866 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/chron_2.3-52.zip'
Content type 'application/zip' length 198130 bytes (193 KB)
downloaded 193 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/sqldf_0.4-11.zip'
Content type 'application/zip' length 78155 bytes (76 KB)
downloaded 76 KB
I also tried to shitch the CRAN but it didn't work.
Many thanks!
I had the exact problem, but I loaded the RGui, ran it as administrator, typed the install command (install.packages("ez") for me), and just let it run. After about 10 solid minutes it finished. Could be you're just not waiting long enough.

knitr installation in R, error

I am fighting Another day with knitr installation and I can not come with new solutions. Last I deleted knitr and tried to install again. Below is a whole console from the process, what is wrong???? I got error message (see below) that is appearing everytime I start R studio and install new packages.
R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Workspace loaded from ~/2016/KNUTSTORP/.RData]
> install.packages("knitr")
Installing package into ‘\\xxxxx.xxxxx/users/Eke/mali/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
also installing the dependencies ‘mime’, ‘stringi’, ‘magrittr’, ‘evaluate’, ‘digest’, ‘formatR’, ‘highr’, ‘markdown’, ‘stringr’, ‘yaml’
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/mime_0.4.zip'
Content type 'application/zip' length 37255 bytes (36 Kb)
opened URL
downloaded 36 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/stringi_1.0-1.zip'
Content type 'application/zip' length 14266706 bytes (13.6 Mb)
opened URL
downloaded 13.6 Mb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/magrittr_1.5.zip'
Content type 'application/zip' length 152098 bytes (148 Kb)
opened URL
downloaded 148 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/evaluate_0.9.zip'
Content type 'application/zip' length 42030 bytes (41 Kb)
opened URL
downloaded 41 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/digest_0.6.9.zip'
Content type 'application/zip' length 171597 bytes (167 Kb)
opened URL
downloaded 167 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/formatR_1.3.zip'
Content type 'application/zip' length 52426 bytes (51 Kb)
opened URL
downloaded 51 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/highr_0.5.1.zip'
Content type 'application/zip' length 35546 bytes (34 Kb)
opened URL
downloaded 34 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/markdown_0.7.7.zip'
Content type 'application/zip' length 165447 bytes (161 Kb)
opened URL
downloaded 161 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/stringr_1.0.0.zip'
Content type 'application/zip' length 83256 bytes (81 Kb)
opened URL
downloaded 81 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/yaml_2.1.13.zip'
Content type 'application/zip' length 180080 bytes (175 Kb)
opened URL
downloaded 175 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/knitr_1.12.3.zip'
Content type 'application/zip' length 811552 bytes (792 Kb)
opened URL
downloaded 792 Kb
package ‘mime’ successfully unpacked and MD5 sums checked
package ‘stringi’ successfully unpacked and MD5 sums checked
package ‘magrittr’ successfully unpacked and MD5 sums checked
package ‘evaluate’ successfully unpacked and MD5 sums checked
package ‘digest’ successfully unpacked and MD5 sums checked
package ‘formatR’ successfully unpacked and MD5 sums checked
package ‘highr’ successfully unpacked and MD5 sums checked
package ‘markdown’ successfully unpacked and MD5 sums checked
package ‘stringr’ successfully unpacked and MD5 sums checked
package ‘yaml’ successfully unpacked and MD5 sums checked
package ‘knitr’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mali\AppData\Local\Temp\RtmpwHvHGn\downloaded_packages
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found
The output of the version
> version
platform i386-w64-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 3
minor 1.2
year 2014
month 10
day 31
svn rev 66913
language R
version.string R version 3.1.2 (2014-10-31)
nickname Pumpkin Helmet
As it was recommended I opened new session. But the Error is still the same. I tested several other packages and they work fine (i.e. nlme, lme4)
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found
[Workspace loaded from ~/R/TESTER/.RData]
What is even more strange is that knitr is somehow installed
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found
[Workspace loaded from ~/R/TESTER/.RData]
> library(knitr)
It does not give an error when loaded by library commend
When I install knitr in Rstudio than I got such comments
Installing packages into '\\xxx.xx/users/Eke/mali/Documents/R/win-library/3.3'
(as 'lib' is unspecified)
also installing the dependencies 'mime', 'stringi', 'magrittr', 'Rcpp'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/mime_0.4.zip'
Content type 'application/zip' length 37402 bytes (36 KB)
==================================================
downloaded 36 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/stringi_1.0-1.zip'
Content type 'application/zip' length 14302873 bytes (13.6 MB)
==================================================
downloaded 13.6 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/magrittr_1.5.zip'
Content type 'application/zip' length 149726 bytes (146 KB)
==================================================
downloaded 146 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/Rcpp_0.12.4.zip'
Content type 'application/zip' length 3249212 bytes (3.1 MB)==================================================
downloaded 3.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/evaluate_0.9.zip'
Content type 'application/zip' length 41981 bytes (40 KB)
==================================================
downloaded 40 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/digest_0.6.9.zip'
Content type 'application/zip' length 169286 bytes (165 KB)
==================================================
downloaded 165 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/formatR_1.3.zip'
Content type 'application/zip' length 52656 bytes (51 KB)
==================================================
downloaded 51 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/highr_0.5.1.zip'
Content type 'application/zip' length 35637 bytes (34 KB)
==================================================
downloaded 34 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/markdown_0.7.7.zip'
Content type 'application/zip' length 167151 bytes (163 KB)==================================================
downloaded 163 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/stringr_1.0.0.zip'
Content type 'application/zip' length 83315 bytes (81 KB)
==================================================
downloaded 81 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/yaml_2.1.13.zip'
Content type 'application/zip' length 175748 bytes (171 KB)
==================================================
downloaded 171 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/htmltools_0.3.5.zip'
Content type 'application/zip' length 571964 bytes (558 KB)==================================================
downloaded 558 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/caTools_1.17.1.zip'
Content type 'application/zip' length 287027 bytes (280 KB)==================================================
downloaded 280 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/bitops_1.0-6.zip'
Content type 'application/zip' length 36372 bytes (35 KB)
==================================================
downloaded 35 KB
package 'mime' successfully unpacked and MD5 sums checked
package 'stringi' successfully unpacked and MD5 sums checked
package 'magrittr' successfully unpacked and MD5 sums checked
package 'Rcpp' successfully unpacked and MD5 sums checked
package 'evaluate' successfully unpacked and MD5 sums checked
package 'digest' successfully unpacked and MD5 sums checked
package 'formatR' successfully unpacked and MD5 sums checked
package 'highr' successfully unpacked and MD5 sums checked
package 'markdown' successfully unpacked and MD5 sums checked
package 'stringr' successfully unpacked and MD5 sums checked
package 'yaml' successfully unpacked and MD5 sums checked
package 'htmltools' successfully unpacked and MD5 sums checked
package 'caTools' successfully unpacked and MD5 sums checked
package 'bitops' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mali\AppData\Local\Temp\RtmpeK2q5y\downloaded_packages
Installing packages into '\\xxxxx.xxxx/users/Eke/mali/Documents/R/win-library/3.3'
(as 'lib' is unspecified)
also installing the dependencies 'mime', 'stringi', 'magrittr', 'Rcpp', 'bitops', 'evaluate', 'digest', 'formatR', 'highr', 'markdown', 'stringr', 'yaml', 'htmltools', 'caTools'
trying URL 'https://cran.rstudio.com/src/contrib/mime_0.4.tar.gz'
Content type 'application/x-gzip' length 12545 bytes (12 KB)
==================================================
downloaded 12 KB
trying URL 'https://cran.rstudio.com/src/contrib/stringi_1.0-1.tar.gz'
Content type 'application/x-gzip' length 3643002 bytes (3.5 MB)==================================================
downloaded 3.5 MB
trying URL 'https://cran.rstudio.com/src/contrib/magrittr_1.5.tar.gz'
Content type 'application/x-gzip' length 200504 bytes (195 KB)==================================================
downloaded 195 KB
trying URL 'https://cran.rstudio.com/src/contrib/Rcpp_0.12.4.tar.gz'
Content type 'application/x-gzip' length 2402065 bytes (2.3 MB)==================================================
downloaded 2.3 MB
trying URL 'https://cran.rstudio.com/src/contrib/bitops_1.0-6.tar.gz'
Content type 'application/x-gzip' length 8734 bytes
==================================================
downloaded 8734 bytes
trying URL 'https://cran.rstudio.com/src/contrib/evaluate_0.9.tar.gz'
Content type 'application/x-gzip' length 19165 bytes (18 KB)
==================================================
downloaded 18 KB
trying URL 'https://cran.rstudio.com/src/contrib/digest_0.6.9.tar.gz'
Content type 'application/x-gzip' length 116746 bytes (114 KB)
==================================================
downloaded 114 KB
trying URL 'https://cran.rstudio.com/src/contrib/formatR_1.3.tar.gz'
Content type 'application/x-gzip' length 28139 bytes (27 KB)==================================================
downloaded 27 KB
trying URL 'https://cran.rstudio.com/src/contrib/highr_0.5.1.tar.gz'
Content type 'application/x-gzip' length 16744 bytes (16 KB)
==================================================
downloaded 16 KB
trying URL 'https://cran.rstudio.com/src/contrib/markdown_0.7.7.tar.gz'
Content type 'application/x-gzip' length 79427 bytes (77 KB)==================================================
downloaded 77 KB
trying URL 'https://cran.rstudio.com/src/contrib/stringr_1.0.0.tar.gz'
Content type 'application/x-gzip' length 34880 bytes (34 KB)
==================================================
downloaded 34 KB
trying URL 'https://cran.rstudio.com/src/contrib/yaml_2.1.13.tar.gz'
Content type 'application/x-gzip' length 81045 bytes (79 KB)
==================================================
downloaded 79 KB
trying URL 'https://cran.rstudio.com/src/contrib/htmltools_0.3.5.tar.gz'
Content type 'application/x-gzip' length 44048 bytes (43 KB)
==================================================
downloaded 43 KB
trying URL 'https://cran.rstudio.com/src/contrib/caTools_1.17.1.tar.gz'
Content type 'application/x-gzip' length 63358 bytes (61 KB)
==================================================
downloaded 61 KB
trying URL 'https://cran.rstudio.com/src/contrib/knitr_1.12.3.tar.gz'
Content type 'application/x-gzip' length 830827 bytes (811 KB)==================================================
downloaded 811 KB
trying URL 'https://cran.rstudio.com/src/contrib/rmarkdown_0.9.6.tar.gz'
Content type 'application/x-gzip' length 2013956 bytes (1.9 MB)==================================================
downloaded 1.9 MB
'\\xxxx.xxx\users\Eke\mali\Documents\R\TESTER'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* installing *source* package 'mime' ...
** package 'mime' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
Warning: running command 'make -f "C:/PROGRA~1/R/R-33~1.0/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-33~1.0/share/make/winshlib.mk" SHLIB="mime.dll" OBJECTS="rawmatch.o"' had status 127
ERROR: compilation failed for package 'mime'
* removing '\\xxxx-xxx/users/Eke/mali/Documents/R/win-library/3.3/mime'
* restoring previous '\\xxxx.xxxx/users/Eke/mali/Documents/R/win-library/3.3/mime'
'\\xxxxx.xxxx\users\Eke\mali\Documents\R\TESTER'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
Warning: running command 'sh ./configure.win' had status 127
ERROR: configuration failed for package 'stringi'
* removing '\\xxxxxxx.xxxx/users/Eke/mali/Documents/R/win-library/3.3/stringi'
* restoring previous '\\xxxxx.xxxx/users/Eke/mali/Documents/R/win-library/3.3/stringi'
'\\xxxxx.xxxxxxx\users\Eke\mali\Documents\R\TESTER'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* installing *source* package 'magrittr' ...
** package 'magrittr' successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
Warning in file(con, "w") :
cannot open file '\\xxxxx.xxxxxx/users/Eke/mali/Documents/R/win-library/3.3/magrittr/doc/index.html': No such file or directory
Error in file(con, "w") : cannot open the connection
ERROR: installing vignettes failed
* removing '\\xxxxx.xxxxx/users/Eke/mali/Documents/R/win-library/3.3/magrittr'
* restoring previous '\\xxxxx.xxxxxx/users/Eke/mali/Documents/R/win-library/3.3/magrittr'
'\\xxxxxx.xxxxxx\users\Eke\mali\Documents\R\TESTER'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* installing *source* package 'Rcpp' ...
** package 'Rcpp' successfully unpacked and MD5 sums checked
I followed #Richie_Cotton proposal without succés
> .libPaths()
[1] "\\\\xxxxx.xxx/users/Eke/mali/Documents/R/win-library/3.3" "C:/Program Files/R/R-3.3.0/library"
> .libPaths("\\\\xxxxxx.xxx/users/Eke/mali/Documents/R/win-library/new")
> .libPaths()
[1] "\\\\xxxxxx.xxx/users/Eke/mali/Documents/R/win-library/new" "C:/Program Files/R/R-3.3.0/library"
> install.packages("knitr", dependencies = F)
Installing package into ‘\\xxxxxx.xxx/users/Eke/mali/Documents/R/win-library/new’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/knitr_1.12.3.zip'
Content type 'application/zip' length 812072 bytes (793 KB)
downloaded 793 KB
package ‘knitr’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mali\AppData\Local\Temp\RtmpmwdUSv\downloaded_packages
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found
>
I user taceback but I do not know how to translate the result
5: stop(gettextf("invalid version specification %s", paste(sQuote(unique(x[!ok])),
collapse = ", ")), call. = FALSE, domain = NA)
4: .make_numeric_version(x, strict, .standard_regexps()$valid_package_version,
"package_version")
3: package_version(utils:::packageDescription(packageName, fields = "Version"))
2: .rs.getPackageVersion("knitr")
1: (function (markdownVersion, stitchVersion)
{
caps <- list()
caps$r_markdown_supported = .rs.scalar(FALSE)
caps$stitch_supported = .rs.scalar(FALSE)
if (.rs.isPackageInstalled("knitr")) {
knitrVersion <- .rs.getPackageVersion("knitr")
caps$r_markdown_supported = .rs.scalar(knitrVersion >=
markdownVersion)
caps$stitch_supported = .rs.scalar(knitrVersion >= stitchVersion)
}
return(caps)
})("1.2", "1.2")
>
It isn't clear from the question where things are going wrong, so you need a strategy to locate the problem. If possible, use the latest version of R for this.
When you install the packages use a fresh session. Additionally, install to a new library location so you can see exactly what is happening. You can always copy the contents of this library over to you existing library afterwards. To do this, create a new directory where you have write permissions (inside your home folder perhaps). Then when you call install.packages, use the lib.loc arguemnt to install to that location.
Rather than calling install.packages("knitr"), install each of the dependencies one by one, to see which one is causing the problem. That is, install.packages("mime"), then install.packages("stringi"), and so on. You can see the list of all the packages that you need in your question (or use packageDescription("knitr").
If you receive an error, use traceback() to see where the error occured, and include these details in your question in you need further help.
Facing the same problem, creating R_LIBS_USER in Windows environmental variables did the trick for me.
See Eric Krantz's comment here. The approach works for both Windows7 and 10.
I copied my knitr folder and its dependencies from
C:\Users\MB\Documents\R\win-library
to
C:\Program Files\R\R-4.1.3\library
Afterwards, I did not have any longer this error message :
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found

Unable to install dplyr package on windows vista

I'm trying to install the dplyr package on my Windows vista machine (through R Studio). I have the latest version of R installed (3.22) and the preview version of R Studio installed. I've had no issues in the past installing packages, however when I try to install this one, I got error:
> install.packages("dplyr")
Installing package into ‘C:/Users/user/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
also installing the dependency ‘BH’
trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/3.2/BH_1.58.0-1.zip'
Content type 'application/zip' length 13846694 bytes (13.2 MB)
downloaded 13.2 MB
trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/3.2/dplyr_0.4.3.zip'
Content type 'application/zip' length 2552598 bytes (2.4 MB)
downloaded 2.4 MB
I also tried installing the devtools package so that I could install the dplyr package straight from github. However, the devtools package also gave me trouble on installation:
> install.packages("devtools")
Installing package into ‘C:/Users/user/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
also installing the dependencies ‘BH’, ‘brew’, ‘xml2’, ‘httr’, ‘curl’, ‘memoise’, ‘whisker’, ‘jsonlite’, ‘roxygen2’, ‘rversions’, ‘git2r’
trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/3.2/BH_1.58.0-1.zip'
Content type 'application/zip' length 13846694 bytes (13.2 MB)
downloaded 13.2 MB
trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/3.2/brew_1.0-6.zip'
Content type 'application/zip' length 104730 bytes (102 KB)
downloaded 102 KB
trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/3.2/xml2_0.1.2.zip'
Content type 'application/zip' length 3174710 bytes (3.0 MB)
downloaded 3.0 MB
trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/3.2/httr_1.0.0.zip'
Content type 'application/zip' length 382429 bytes (373 KB)
downloaded 373 KB
trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/3.2/curl_0.9.3.zip'
Content type 'application/zip' length 4384906 bytes (4.2 MB)
downloaded 4.2 MB
trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/3.2/memoise_0.2.1.zip'
Content type 'application/zip' length 16878 bytes (16 KB)
downloaded 16 KB
trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/3.2/whisker_0.3-2.zip'
Content type 'application/zip' length 64756 bytes (63 KB)
downloaded 63 KB
trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/3.2/jsonlite_0.9.17.zip'
Content type 'application/zip' length 1009755 bytes (986 KB)
downloaded 986 KB
trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/3.2/roxygen2_4.1.1.zip'
Content type 'application/zip' length 594453 bytes (580 KB)
downloaded 580 KB
trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/3.2/rversions_1.0.2.zip'
Content type 'application/zip' length 16455 bytes (16 KB)
downloaded 16 KB
trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/3.2/git2r_0.11.0.zip'
Content type 'application/zip' length 2690457 bytes (2.6 MB)
downloaded 2.6 MB
trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/3.2/devtools_1.9.1.zip'
Content type 'application/zip' length 357684 bytes (349 KB)
downloaded 349 KB
None of these files ever get written into ‘C:/Users/user/Documents/R/win-library/3.2’.
Other things tried:
making sure that I have the latest version of R installed
opening R Studio in Administrator mode and installing the packages then
installing in R commander instead
trying a different CRAN mirror
None of these helped.
Any ideas how to install dplyr?
As #erasmortg suggested in the comments, I first downloaded the dplyr zip file from the cran-r page. Then ran:
utils::install.packages("c:/R/dplyrversion.zip", repos=NULL)

can't install "CHAID" on Mac OS X 10.9.5

I have encountered a problem of installing CHAID package on my Mac. I am not sure if it is a problem of my Mac OS version or some other problems. Could anyone help?
Thank you so much!!
install.packages("CHAID", repos="http://R-Forge.R-project.org")
Warning in install.packages :
cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://R-Forge.R-project.org/bin/macosx/mavericks/contrib/3.1
package ‘CHAID’ is available as a source package but not as a binary
Warning in install.packages :
package ‘CHAID’ is not available (for R version 3.1.2)
You first need to install the 'partykit' package (and all of its dependincies) and then issue this command:
install.packages("CHAID", repos="http://R-Forge.R-project.org", type="source")
This is the transcript on a Yosemite machine but I think this should also succeed on Mavericks. (You can notice that there is no invocation of compiled code, so I do not need to warn you that XCode might be needed.)
> install.packages("CHAID", repos="http://R-Forge.R-project.org", type="source")
Warning: dependency ‘partykit’ is not available
trying URL 'http://R-Forge.R-project.org/src/contrib/CHAID_0.1-1.tar.gz'
Content type 'application/x-gzip' length 356348 bytes (347 KB)
opened URL
==================================================
downloaded 347 KB
ERROR: dependency ‘partykit’ is not available for package ‘CHAID’
* removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/CHAID’
The downloaded source packages are in
‘/private/var/folders/yq/m3j1jqtj6hq6s5mq_v0jn3s80000gp/T/RtmpMD0mfx/downloaded_packages’
Warning message:
In install.packages("CHAID", repos = "http://R-Forge.R-project.org", :
installation of package ‘CHAID’ had non-zero exit status
also installing the dependencies ‘RWekajars’, ‘pmml’, ‘strucchange’, ‘mlbench’, ‘RWeka’, ‘psychotools’, ‘psychotree’
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.1/RWekajars_3.7.12-1.tgz'
Content type 'application/x-gzip' length 6562134 bytes (6.3 MB)
opened URL
==================================================
downloaded 6.3 MB
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.1/pmml_1.4.2.tgz'
Content type 'application/x-gzip' length 184357 bytes (180 KB)
opened URL
==================================================
downloaded 180 KB
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.1/strucchange_1.5-0.tgz'
Content type 'application/x-gzip' length 784786 bytes (766 KB)
opened URL
==================================================
downloaded 766 KB
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.1/mlbench_2.1-1.tgz'
Content type 'application/x-gzip' length 1021909 bytes (997 KB)
opened URL
==================================================
downloaded 997 KB
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.1/RWeka_0.4-24.tgz'
Content type 'application/x-gzip' length 533932 bytes (521 KB)
opened URL
==================================================
downloaded 521 KB
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.1/psychotools_0.4-0.tgz'
Content type 'application/x-gzip' length 353913 bytes (345 KB)
opened URL
==================================================
downloaded 345 KB
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.1/psychotree_0.15-0.tgz'
Content type 'application/x-gzip' length 257879 bytes (251 KB)
opened URL
==================================================
downloaded 251 KB
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.1/partykit_0.8-4.tgz'
Content type 'application/x-gzip' length 1194059 bytes (1.1 MB)
opened URL
==================================================
downloaded 1.1 MB
The downloaded binary packages are in
/var/folders/yq/m3j1jqtj6hq6s5mq_v0jn3s80000gp/T//RtmpMD0mfx/downloaded_packages
> install.packages("CHAID", repos="http://R-Forge.R-project.org", type="source")
trying URL 'http://R-Forge.R-project.org/src/contrib/CHAID_0.1-1.tar.gz'
Content type 'application/x-gzip' length 356348 bytes (347 KB)
opened URL
==================================================
downloaded 347 KB
* installing *source* package ‘CHAID’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (CHAID)
The downloaded source packages are in
‘/private/var/folders/yq/m3j1jqtj6hq6s5mq_v0jn3s80000gp/T/RtmpMD0mfx/downloaded_packages’
>

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