The directory is not writable — данная ошибка означает, что каталог не доступен для записи. Например это каталог который содержит файл(ы) с логами, кэшем и т.д. Обычно ошибка выглядит примерно так:
The directory is not writable by the Web process /var/www/web/assets
Где /var/www/web/assets – это путь к папке, к которой необходимо разрешить доступ.
Часто эта ошибка возникает при неправильном распределении прав доступа к папкам (файлам) на хостинге или сервере. Кстати, могу порекомендовать недорогой хостинг.
Текст такого цвета является примером, который в вашем случае может отличаться.
Если вы используете локальный Веб-сервер, в моем случае это Ubuntu 14.04 TLS, проблема решается назначением полных прав:
sudo chmod 777 /var/www/web/assets
Для обеспечения безопасности на рабочем сервере (в глобальной сети) хостинге/сервере вместо 777 используйте 755.
Используя сайт abuzov.ru, вы даете согласие на работу с cookie, Яндекс.Метрикой, Google Analytics для сбора технических данных.OKПодробнее
I installed the Bioconductor packages on R version 3.1.2 on Ubuntu 14.04 and received the message below:
The downloaded source packages are in
‘/tmp/RtmpZYw0Qp/downloaded_packages’ Warning message: installed
directory not writable, cannot update packages ‘boot’, ‘class’,
‘KernSmooth’, ‘mgcv’, ‘nnet’, ‘rpart’, ‘spatial’
What does it mean, and how does it affect using the above packages on R?
Roman Luštrik
68.5k24 gold badges153 silver badges195 bronze badges
asked Feb 16, 2015 at 16:51
1
I faced the same problem working in R-studio. The solution is to give root access to R.
In Windows, that means you need to run the program as an Administrator.
In Unix/Linux, you should launch R from the terminal by doing sudo R.
Then, once you’re running with sufficient privileges, you can try installing your package and it should work.
Cody Gray♦
236k50 gold badges486 silver badges567 bronze badges
answered Feb 16, 2016 at 19:41
NinadmwNinadmw
1011 silver badge2 bronze badges
The warning means that there are more recent versions of the listed packages available, but your version cannot be updated because the directory in which the packages are installed cannot be written to. Usually this means that R was installed with ‘system administrator’ privileges, but that you are trying to update packages as a regular user.
The consequence is that the features or bug fixes implemented in the updated packages are not available to you. The specific consequences could range from minor typographical corrections on a man page through serious bug fixes. Qualitatively, my bet is that it ‘does not matter’ for most uses.
The solution is to update these packages when running R as a user with permission to write to packages in the installed directories — typically the last element of the output of .libPaths(), or more fine-grained via installed.packages()[, "LibPath"]
answered Feb 16, 2015 at 17:57
Martin MorganMartin Morgan
45.6k7 gold badges81 silver badges110 bronze badges
2
I faced the same problem today when installing three Bioconductor packages under Windows. Two (dependencies of the package I really wanted) were already on my system in newer forms (as described in @Martin-Morgan solution) and so no action was necessary. However, one was not installed. For this, third package, I had success in doing an installation from the local file that was downloaded during the failed install without having to escalate privileges (which was my next step as outlined by @Ninadmw).
In R, go to the menu Packages/Install Package(s) from local files and navigate to the local download directory listed, which in your case was /tmp/RtmpZYw0Qp/downloaded_packages, and select the package you want to install.
In RStudio (which you should use), go to the menu ToolsInstall Packages, change the install from field to Package Archive File (.zip; .tar.gz), use Browse... to navigate to the listed download directory, which in your case was /tmp/RtmpZYw0Qp/downloaded_packages and select the package you want to install. Then click on the Install button.
answered Dec 30, 2016 at 14:53
Jim QuirkJim Quirk
5564 silver badges18 bronze badges
R windows FAQ documents this behavior:
http://cran.r-project.org/bin/windows/base/rw-FAQ.html
2.24 Does R run under Windows Vista/7/8/Server 2008?
…
If you install R as a standard user into your own file space and use it under the same account, there are no known permission issues.
If you use the default Administrator account (without ‘admin approval mode’ being turned on) and install/update packages (in the system area or elsewhere), no issues are known.
If you use an account in the local Administrators group in ‘admin approval mode’ (which is the intended norm under these OSes), installation will make use of ‘over-the-shoulder’ credentials. You will run into problems if you try installing (including updating) packages in the main R library. (It would be nice if at that point R could use over-the-shoulder credentials, but they apply to processes as a whole. Vista and later disallow creating .dll files in the system area without credentials.) There are several ways around this.
Run R with Administrator privileges in sessions where you want to install packages. (Do so by right-clicking on the R shortcut and selecting ’Run as Administrator’.)
Transfer ownership of the R installation to the user which installed R. To do so, use the security tab on the ‘Properties’ of the top-level R folder and give ‘Full Control’ over this directory to the user (not just the Administrator group).
Install packages into a different library tree owned by the account used to install R.
For an installation to be used by a single user, the simplest way is to make use of a ‘personal library’: See I don’t have permission to write to the R-3.2.0library directory.
…
Главная / ОС / FreeBSD / Ошибка Named: the working dire…
Просматривая сообщения системы при старте при помощи # dmesg -a, обнаружил ошибку: Named: the working directory is not writable. Как понятно из самого сообщения, сервер имен сообщает, что его рабочая директория не доступна для записи. Несмотря на эту ошибку Named работал без проблем и выполнял свои функциональные обязанности.
Руководствуясь принципом: «Чем меньше ошибок, тем спокойнее администратору» я начал искать причину возникновения и пути устранения неполадки. Попытавшись найти лог-файл Named, обнаружилось, что таковой отсутствует. Точнее, информация попадает в общий лог-файл /var/log/messages. Почему DirectAdmin не логирует достаточно важный сервис системы отдельным логом — загадка, но исправить этот недосмотр можно довольно таки просто. Описание наиболее важных логов DA, с которых разработчики панели управления рекомендуют начинать «разбор полетов» находится тут: log-файлы DirectAdmin.
Чтобы вести отдельный лог Named, в файл /etc/syslog.conf нужно добавить две строчки:
!named
*.* /var/log/named.log
После чего, необходимо создать лог-файл для Bind, установить для него владельца и группу bind и перезапустить процесс syslogd:
#touch /var/log/named.log
#chown bind:bind /var/log/named.log
#/etc/rc.d/syslogd restart
Теперь, после перезапуска сервера имен Named (можно выполнить из панели управления DirectAdmin: Admin Level -> Service Monitor -> named restart), в лог файл запишется информация о работе сервиса. Правда, к сожалению, ошибка «the working directory is not writable» оказалась и там. Чтобы её исправить, необходимо сменить права на рабочую директорию Named. Поискав эту директорию в /etc, я обнаружил там только символическую ссылку на необходимую директорию — сама директория располагается тут: /var/named/etc/namedb. После запуска смены владельца и перезагрузке Named ошибка из лог-файла исчезла:
# chown bind:bind /var/named/etc/namedb
Изменять владельца стоит только на рабочую директорию Named — все её файлы и поддиректории можно оставить как есть.
Создать отдельный лог-файл Named и устранить ошибки Named помогла статья с сайта: lissyara.su, за которую её автору нужно сказать «Спасибо»!
P.S. Как сообщают официальные источники из DA — ошибка «Named: the working directory is not writable» может всплыть в будущем, но обращать на неё внимание не стоит.
Опубликовано: 2012/09/19
HTML-код ссылки на эту страницу:
<a href=»https://petrenco.com/freebsd.php?txt=152″ target=»_blank»>Ошибка Named: the working directory is not writable (FreeBSD + DirectAdmin)</a>
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warning directory not writable
@eric-p-5199
Last seen 7.7 years ago
Sweden
Hej
I am reinstalling bioconductor because I needed to reinstall my OS due to some complications and I am experiencing some complications.
I cannot install some of the packages and get this output at the end
The downloaded source packages are in
‘/tmp/Rtmpn4Uw0m/downloaded_packages’
Warning message:
installed directory not writable, cannot update packages ‘affy’,
‘affyio’, ‘AnnotationDbi’, ‘Biobase’, ‘BiocInstaller’, ‘biovizBase’,
‘chron’, ‘colorspace’, ‘DBI’, ‘digest’, ‘fastcluster’, ‘Formula’,
‘GenomicFeatures’, ‘GenomicRanges’, ‘ggplot2’, ‘graph’, ‘Hmisc’,
‘hwriter’, ‘hypergraph’, ‘IRanges’, ‘labeling’, ‘limma’,
‘makecdfenv’, ‘plyr’, ‘preprocessCore’, ‘RColorBrewer’, ‘RCurl’,
‘reshape2’, ‘Rsamtools’, ‘RSQLite’, ‘rtracklayer’, ‘scales’,
‘statmod’, ‘tcltk2’, ‘tgp’, ‘cluster’, ‘lattice’, ‘MASS’, ‘rpart’
Any ideas what the problem is ??
installation
• 2.2k views
@patrick-schorderet-6081
Last seen 7.7 years ago
United States
Are you using a personal computer or one belonging to the institute? Do you have admin privileges on R?
@eric-p-5199
Last seen 7.7 years ago
Sweden
I am using a personal computer, how do I check if I have admin privileges on R?
I tried sudo R and then installing affy for example and it seems to be working.
So basically I installed R, without admin privilages, how is that even possible when I used sudo apt-get install?
Do you think you could tell me how I can change the admin privilages. I am only running linux mint on this computer if that makes a difference.
I have another problem now with installing OneChannelGUI, I get this error when it is installing:
ucsc/zlibFace.c:4:18: fatal error: zlib.h: No such file or directory #include <zlib.h>
these are my warnings
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ‘tkrplot’ had non-zero exit status 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ‘affyPLM’ had non-zero exit status 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ‘affylmGUI’ had non-zero exit status 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ‘oneChannelGUI’ had non-zero exit status 5: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘affyio’ had non-zero exit status 6: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘preprocessCore’ had non-zero exit status 7: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘RCurl’ had non-zero exit status 8: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘Rsamtools’ had non-zero exit status 9: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘statmod’ had non-zero exit status 10: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘tgp’ had non-zero exit status 11: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘rtracklayer’ had non-zero exit status 12: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘GenomicFeatures’ had non-zero exit status 13: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘cluster’ had non-zero exit status
I can make another thread if no one asnwers it
thanks
@eric-p-5199
Last seen 7.7 years ago
Sweden
I finally managed to figure it out. Linux mint has an older version in its dependencies, so I had to purge everything and reinstall the newer version. Then reinstall many packages that don’t install automatically.
I am still not able to install Rcurl, but I can run bioconductor so no worries I guess
Thanks for the help
Login before adding your answer.
I installed the Bioconductor packages on R version 3.1.2 on Ubuntu 14.04 and received the message below:
The downloaded source packages are in
‘/tmp/RtmpZYw0Qp/downloaded_packages’ Warning message: installed
directory not writable, cannot update packages ‘boot’, ‘class’,
‘KernSmooth’, ‘mgcv’, ‘nnet’, ‘rpart’, ‘spatial’
What does it mean, and how does it affect using the above packages on R?
Roman Luštrik
69.3k24 gold badges152 silver badges195 bronze badges
asked Feb 16, 2015 at 16:51
Elizabeth NyamuElizabeth Nyamu
1011 gold badge2 silver badges4 bronze badges
1
I faced the same problem working in R-studio. The solution is to give root access to R.
In Windows, that means you need to run the program as an Administrator.
In Unix/Linux, you should launch R from the terminal by doing sudo R.
Then, once you’re running with sufficient privileges, you can try installing your package and it should work.
answered Feb 16, 2016 at 19:41
The warning means that there are more recent versions of the listed packages available, but your version cannot be updated because the directory in which the packages are installed cannot be written to. Usually this means that R was installed with ‘system administrator’ privileges, but that you are trying to update packages as a regular user.
The consequence is that the features or bug fixes implemented in the updated packages are not available to you. The specific consequences could range from minor typographical corrections on a man page through serious bug fixes. Qualitatively, my bet is that it ‘does not matter’ for most uses.
The solution is to update these packages when running R as a user with permission to write to packages in the installed directories — typically the last element of the output of .libPaths(), or more fine-grained via installed.packages()[, "LibPath"]
answered Feb 16, 2015 at 17:57
Martin MorganMartin Morgan
45.9k7 gold badges84 silver badges112 bronze badges
2
I faced the same problem today when installing three Bioconductor packages under Windows. Two (dependencies of the package I really wanted) were already on my system in newer forms (as described in @Martin-Morgan solution) and so no action was necessary. However, one was not installed. For this, third package, I had success in doing an installation from the local file that was downloaded during the failed install without having to escalate privileges (which was my next step as outlined by @Ninadmw).
In R, go to the menu Packages/Install Package(s) from local files and navigate to the local download directory listed, which in your case was /tmp/RtmpZYw0Qp/downloaded_packages, and select the package you want to install.
In RStudio (which you should use), go to the menu ToolsInstall Packages, change the install from field to Package Archive File (.zip; .tar.gz), use Browse... to navigate to the listed download directory, which in your case was /tmp/RtmpZYw0Qp/downloaded_packages and select the package you want to install. Then click on the Install button.
answered Dec 30, 2016 at 14:53
Jim QuirkJim Quirk
5714 silver badges18 bronze badges
The directory is not writable — данная ошибка означает, что каталог не доступен для записи. Например это каталог который содержит файл(ы) с логами, кэшем и т.д. Обычно ошибка выглядит примерно так:
The directory is not writable by the Web process /var/www/web/assets
Где /var/www/web/assets – это путь к папке, к которой необходимо разрешить доступ.
Часто эта ошибка возникает при неправильном распределении прав доступа к папкам (файлам) на хостинге или сервере. Кстати, могу порекомендовать недорогой хостинг.
Текст такого цвета является примером, который в вашем случае может отличаться.
Если вы используете локальный Веб-сервер, в моем случае это Ubuntu 14.04 TLS, проблема решается назначением полных прав:
sudo chmod 777 /var/www/web/assets
Для обеспечения безопасности на рабочем сервере (в глобальной сети) хостинге/сервере вместо 777 используйте 755.
Используя сайт abuzov.ru, вы даете согласие на работу с cookie, Яндекс.Метрикой, Google Analytics для сбора технических данных.OKПодробнее
R windows FAQ documents this behavior:
http://cran.r-project.org/bin/windows/base/rw-FAQ.html
2.24 Does R run under Windows Vista/7/8/Server 2008?
…
If you install R as a standard user into your own file space and use it under the same account, there are no known permission issues.
If you use the default Administrator account (without ‘admin approval mode’ being turned on) and install/update packages (in the system area or elsewhere), no issues are known.
If you use an account in the local Administrators group in ‘admin approval mode’ (which is the intended norm under these OSes), installation will make use of ‘over-the-shoulder’ credentials. You will run into problems if you try installing (including updating) packages in the main R library. (It would be nice if at that point R could use over-the-shoulder credentials, but they apply to processes as a whole. Vista and later disallow creating .dll files in the system area without credentials.) There are several ways around this.
Run R with Administrator privileges in sessions where you want to install packages. (Do so by right-clicking on the R shortcut and selecting ’Run as Administrator’.)
Transfer ownership of the R installation to the user which installed R. To do so, use the security tab on the ‘Properties’ of the top-level R folder and give ‘Full Control’ over this directory to the user (not just the Administrator group).
Install packages into a different library tree owned by the account used to install R.
For an installation to be used by a single user, the simplest way is to make use of a ‘personal library’: See I don’t have permission to write to the R-3.2.0library directory.
…
warning directory not writable
@eric-p-5199
Last seen 8.1 years ago
Sweden
Hej
I am reinstalling bioconductor because I needed to reinstall my OS due to some complications and I am experiencing some complications.
I cannot install some of the packages and get this output at the end
The downloaded source packages are in
‘/tmp/Rtmpn4Uw0m/downloaded_packages’
Warning message:
installed directory not writable, cannot update packages ‘affy’,
‘affyio’, ‘AnnotationDbi’, ‘Biobase’, ‘BiocInstaller’, ‘biovizBase’,
‘chron’, ‘colorspace’, ‘DBI’, ‘digest’, ‘fastcluster’, ‘Formula’,
‘GenomicFeatures’, ‘GenomicRanges’, ‘ggplot2’, ‘graph’, ‘Hmisc’,
‘hwriter’, ‘hypergraph’, ‘IRanges’, ‘labeling’, ‘limma’,
‘makecdfenv’, ‘plyr’, ‘preprocessCore’, ‘RColorBrewer’, ‘RCurl’,
‘reshape2’, ‘Rsamtools’, ‘RSQLite’, ‘rtracklayer’, ‘scales’,
‘statmod’, ‘tcltk2’, ‘tgp’, ‘cluster’, ‘lattice’, ‘MASS’, ‘rpart’
Any ideas what the problem is ??
installation
• 2.3k views
@patrick-schorderet-6081
Last seen 8.1 years ago
United States
Are you using a personal computer or one belonging to the institute? Do you have admin privileges on R?
@eric-p-5199
Last seen 8.1 years ago
Sweden
I am using a personal computer, how do I check if I have admin privileges on R?
I tried sudo R and then installing affy for example and it seems to be working.
So basically I installed R, without admin privilages, how is that even possible when I used sudo apt-get install?
Do you think you could tell me how I can change the admin privilages. I am only running linux mint on this computer if that makes a difference.
I have another problem now with installing OneChannelGUI, I get this error when it is installing:
ucsc/zlibFace.c:4:18: fatal error: zlib.h: No such file or directory #include <zlib.h>
these are my warnings
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ‘tkrplot’ had non-zero exit status 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ‘affyPLM’ had non-zero exit status 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ‘affylmGUI’ had non-zero exit status 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ‘oneChannelGUI’ had non-zero exit status 5: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘affyio’ had non-zero exit status 6: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘preprocessCore’ had non-zero exit status 7: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘RCurl’ had non-zero exit status 8: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘Rsamtools’ had non-zero exit status 9: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘statmod’ had non-zero exit status 10: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘tgp’ had non-zero exit status 11: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘rtracklayer’ had non-zero exit status 12: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘GenomicFeatures’ had non-zero exit status 13: In install.packages(update[instlib == l, "Package"], l, ... : installation of package ‘cluster’ had non-zero exit status
I can make another thread if no one asnwers it
thanks
@eric-p-5199
Last seen 8.1 years ago
Sweden
I finally managed to figure it out. Linux mint has an older version in its dependencies, so I had to purge everything and reinstall the newer version. Then reinstall many packages that don’t install automatically.
I am still not able to install Rcurl, but I can run bioconductor so no worries I guess
Thanks for the help
Login before adding your answer.