I have the problem of upgrading my phpunit with pyrus, and it always output something like:
Pyrus\Installer\Exception: Dependency validation failed for some packages to install, installation aborted
Pyrus\Dependency\Exception: pear.phpunit.de/PHPUnit requires package "channel://pear.phpunit.de/PHP_CodeCoverage" (version >= 1.2.1), installed version is 1.2.0
Pyrus\Dependency\Exception: pear.phpunit.de/PHPUnit can optionally use package "channel://pear.phpunit.de/PHP_Invoker" (version >= 1.1.0)
I have use the -f flag to force upgrade my phpunit from 3.7.0 to 3.7.1, but other packages still not upgrade.
I have tried to use the command php pyrus.phar upgrade phpunit/PHP_CodeCoverage to upgrade PHP_CodeCoverage, but I got the something like:
Skipping installed package pear.phpunit.de/PHP_CodeCoverage
How can I upgrade ohter package separatly?
Try --alldeps flag, should help: http://pear.php.net/manual/en/guide.users.commandline.installing.php
Related
cannot install phytools
tried with devtools
library(devtools)
install_github("liamrevell/phytools")
and
install.packages("phytools")
I keep getting the same error
ERROR: dependency ‘mnormt’ is not available for package ‘phytools’
and I cannot install mnormt because
package ‘mnormt’ is not available (for R version 3.6.3)
gfortran is already installed in my system
GNU Fortran (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0
any help is highly appreciated,
thanks
On Ubuntu Linux I cannot get R to update to the latest version (>4.0 at the time of writing), so, like Dirk suggests I have to install an older version of the package, one compatible with the version of R I am running.
My R version is 3.6.3, released feb 2020
I go to the mnormt page and click on "old sources" https://cran.r-project.org/src/contrib/Archive/mnormt/
I see that version 1.5-6 is the most recent release which is prior to my version of R
Following these pages: "Installing older versions of packages" https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages I copy the relevant url into this code and run it in R
packageurl <- "https://cran.r-project.org/src/contrib/Archive/mnormt/mnormt_1.5-6.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
Which fixes my problem installing mnormt and also allows packages which depend on it to be installed in the standard way (as far as I tested it)
The current version of mnormt depends on a the current version of R; you chose to remain a version behind.
So just install the previous version of mnormt, for example via
cd /tmp
wget https://cran.r-project.org/src/contrib/Archive/mnormt/mnormt_1.5-7.tar.gz
R CMD INSTALL mnormt_1.5-7.tar.gz
Prefix that last INSTALL command with sudo, or change the permission/group membership of /usr/local/lib/R/site-library, if R tells you it cannot write there.
Once mnormt is installed, proceed with the installation of phytools.
Try to add the tag version to install command, for example: devtools::install_github('cran/mnormt#R-3.0.3')
Check what version you need and replace the tag after the '#'.
I need to install few packages that should be installed with remotes::install_github() like
"acidgenomics/basejump" or "satijalab/seurat".
During the installation, it need to upgrade few other packages version. The BiocManager::install program cannot find those versions and I had to install those dependencies packages version with:
R CMD INSTALL IRanges_2.20.2.tar.gz
Then other packages, that use the same packages stop working. like DESeq2,
I get the error:
Error: package or namespace load failed for ‘DESeq2’:
objects ‘rowSums’, ‘colSums’, ‘rowMeans’, ‘colMeans’ are not exported by 'namespace:S4Vectors'
I found few answers that say it happen (like url)
remotes::install_github() isn't picking up the correct Bioconductor
devel repos, whereas installing with BiocManager::install() does work
as expected.
we have the R 3.6.0 installed as a module and a lot of users uses the same R version. I need all packages to work for everyone.
How can I make all variety packages versions to work?
Finally, I install new version of R 3.6.3 with Bioconductor 3.10 and all the packages install right.
I follow the instructions to install meteor 1.6 on Windows(10) as stated on Meteor.com (choco install meteor) and it's installed a meteor v0.0.2 ?
When I try to run any meteor command I get: bash: meteor: command not found
and when I try choco upgrade meteor I get:
$ choco upgrade meteor
Chocolatey v0.10.8
Upgrading the following packages:
meteor
By upgrading you accept licenses for the packages.
meteor v0.0.2 is the latest version available based on your source(s).
Chocolatey upgraded 0/1 packages.
See the log for details (C:\ProgramData\chocolatey\logs\chocolatey.log).
I tried choco uninstall meteor and then reinstall choco instlal meteor but same issue. Searching around online a little I found this page:
https://chocolatey.org/packages/meteor
I do have meteor installed and running on version 1.6.0.1 on Window 10's Ubuntu bash which was installed via curl https://install.meteor.com/ | sh
Following on from above post https://stackoverflow.com/a/47967277/642729 by Gary Ewan Park. The below comment on https://chocolatey.org/packages/meteor clarifies the Chocolately/Meteor versioning
The current version of Meteor is 1.6;
is this the version in the 0.0.2 Chocolatey package?
[Garrie Powers • 2 months ago]
The version number of the Chocolatey package is the version of the installer.
Meteor is unique in the way it works in that all versions
are capable of springboarding to other versions.
Therefore, in the same way as the Unix installer installs the latest version,
the Chocolatey installer will always install the latest version.
So at this exact moment, the answer to your question is "yes"!
[Jesse Rosenberger Garrie Powers • 2 months ago]
The best advice would be to reach out to the maintainers of that package of chocolatey.org. This can be done by clicking on the "Contact Maintainers" link of this page:
https://chocolatey.org/packages/meteor
It would seem that the creators of the application, also own the Chocolatey package, so hopefully they will get back to you.
From the official installer github:
The version of this Meteor installer is not to be confused with Meteor itself. Meteor, once installed, will always "springboard" to (download, install and run) the correct version of Meteor necessary for the application being executed.
...
When necessary, specific versions of Meteor can be installed using
Chocoloatey's --params argument which will download that specific
version from Meteor's installation server. For example, to install
Meteor 1.5.4.4:
C:> choco install meteor --params="'/RELEASE:1.6.0.1'"
Note: Prior to
Meteor 1.6, 64-bit versions were not available. Therefore, in order to
install versions prior to Meteor 1.6, you'll also need to pass
Chocolatey's --x86 option when running choco install on 64-bit Windows
platforms. For example:
C:> choco install meteor --x86 --params="'/RELEASE:1.5.4.4'"
For two days I've been trying to install Openblas/atlas with Lapack and use it in R. it's driving me crazy. I'm at a point where I can't even think anymore.
My server uses:
Red Hat Enterprise Linux Server release 6.6 (Santiago)
Here is what I've installed so far:
[root#tpdb05 atlas]# yum install atlas.x86_64 blas.x86_64 lapack.x86_64 Loaded plugins: product-id, refresh-packagekit, rhnplugin, security, subscription-manager
Setting up Install Process
Package atlas-3.8.4-2.el6.x86_64 already installed and latest version
Package blas-3.2.1-4.el6.x86_64 already installed and latest version
Package lapack-3.2.1-4.el6.x86_64 already installed and latest version
[root#tpdb05 ruser]#
yum install lapack.i686
Installed:
lapack.i686 0:3.2.1-4.el6
Dependency Installed:
blas.i686 0:3.2.1-4.el6 glibc.i686 0:2.12-1.166.el6_7.3 libgfortran.i686 0:4.4.7-16.el6
nss-softokn-freebl.i686 0:3.14.3-23.el6_7
Dependency Updated:
glibc.x86_64 0:2.12-1.166.el6_7.3 glibc-common.x86_64 0:2.12-1.166.el6_7.3 glibc-devel.x86_64 0:2.12-1.166.el6_7.3
glibc-headers.x86_64 0:2.12-1.166.el6_7.3 nss-softokn-freebl.x86_64 0:3.14.3-23.el6_7
yum install atlas.i686
Installed:
atlas.i686 0:3.8.4-2.el6
[root#tpdb05 SRPMS]# yum install rpm-build
Installed:
rpm-build.x86_64 0:4.8.0-47.el6
Dependency Installed:
redhat-rpm-config.noarch 0:9.0.3-44.el6
Dependency Updated:
rpm.x86_64 0:4.8.0-47.el6 rpm-libs.x86_64 0:4.8.0-47.el6 rpm-python.x86_64 0:4.8.0-47.el6
[root#tpdb05 SRPMS]# yum install atlas-c++-devel.x86_64
Installed:
atlas-c++-devel.x86_64 0:0.6.1-1.el5.rf
Dependency Installed:
atlas-c++.x86_64 0:0.6.1-1.el5.rf
several sources I've tried without success:
1 2 3
The R manual mentions the following:
The usual way to specify ATLAS will be via
--with-blas="-lf77blas -latlas"
However I have no clue where to use this command. While installing R? I'm pretty sure it should be possible to simply swap between libraries..
How do I get R to use the atlas/openblas/lapack libraries?
The current version of PHPUnit is 3.6, but until I update my code I need to use 3.5.15 instead. I'm having a lot of trouble trying to get 3.5.15 installed.
I start with a clean install of Zend Server, which only has a few basic PEAR packages installed. I channel-discover pear.phpunit.de and pear.symfony-project.com. Then I try installing 3.5.15 from a URL, but it fails:
# pear install http://pear.phpunit.de/get/PHPUnit-3.5.15.tgz
downloading PHPUnit-3.5.15.tgz ...
Duplicate package channel://pear.phpunit.de/PHPUnit-3.5.15 found
Duplicate package channel://pear.phpunit.de/PHPUnit-3.6.0 found
install failed
Next, I try installing from a downloaded file, but that also fails:
# pear install ~/Desktop/PHPUnit-3.5.15.tgz
Duplicate package channel://pear.phpunit.de/PHPUnit-3.5.15 found
Duplicate package channel://pear.phpunit.de/PHPUnit-3.6.0 found
install failed
And then from PEAR directly ... which installs 3.6 instead of what I asked for!
# pear install phpunit/PHPUnit-3.5.15
phpunit/PHPUnit can optionally use package "pear/XML_RPC2"
phpunit/PHPUnit can optionally use PHP extension "dbus"
phpunit/DbUnit requires package "phpunit/PHPUnit" (version >= 3.6.0), downloaded version is 3.5.15
phpunit/PHPUnit requires package "phpunit/DbUnit" (version >= 1.0.0)
phpunit/PHPUnit can optionally use package "phpunit/PHP_Invoker" (version >= 1.0.0)
downloading File_Iterator-1.3.0.tgz ...
downloading Text_Template-1.1.1.tgz ...
downloading PHP_CodeCoverage-1.1.0.tgz ...
downloading PHP_Timer-1.0.2.tgz ...
downloading PHPUnit_MockObject-1.1.0.tgz ...
downloading PHPUnit_Selenium-1.1.0.tgz ...
downloading YAML-1.0.6.tgz ...
downloading PHPUnit-3.6.0.tgz ...
downloading PHP_TokenStream-1.1.0.tgz ...
install ok: channel://pear.phpunit.de/File_Iterator-1.3.0
install ok: channel://pear.phpunit.de/Text_Template-1.1.1
install ok: channel://pear.phpunit.de/PHP_Timer-1.0.2
install ok: channel://pear.symfony-project.com/YAML-1.0.6
install ok: channel://pear.phpunit.de/PHP_TokenStream-1.1.0
install ok: channel://pear.phpunit.de/PHP_CodeCoverage-1.1.0
install ok: channel://pear.phpunit.de/PHPUnit_MockObject-1.1.0
install ok: channel://pear.phpunit.de/PHPUnit-3.6.0
install ok: channel://pear.phpunit.de/PHPUnit_Selenium-1.1.0
Even using the -f option, to try to force an installation of the version I asked for, doesn't change anything.
How do I get 3.5.15 installed?
There are a lot of dependencies you have to deal with to have Pear NOT forcibly install PHPUnit 3.6. Here's what I did to get PHPUnit 3.5.15 installed: http://dustyreagan.com/downgrade-phpunit-3-6-to-3-5-15/
PHPUnit-3.5.15 requires DbUnit, but the latest version of DbUnit (1.1.0) requires PHPUnit-3.6. So that's why, when I installed PHPUnit 3.5.15, 3.6 would be installed instead. I worked around the problem by specifically installing DbUnit-1.0.3.
I'll accept my own answer, but it's not a complete answer - an attempt to install PHPUnit 3.5 results in the installation of a module which then forces the install of PHPUnit 3.6, and that doesn't seem right. This looks like a packaging problem, but I couldn't figure out where to report it.
I have not been able to install PHPUnit correctly on Ubuntu
Am installing on widnows 7 now
following advice from here
http://dustyreagan.com/downgrade-phpunit-3-6-to-3-5-15/
and abstracting it :) now hopeful that I will be able to install upon
ubuntu too
--
It worked now have phpunit correct version installed.
To get the question from the unanswered list:
PHPUnit-3.5.15 requires DbUnit, but the latest version of DbUnit (1.1.0) requires PHPUnit-3.6.
So that's why, when I installed PHPUnit 3.5.15, 3.6 would be installed instead. I worked around the problem by specifically installing DbUnit-1.0.3
This worked fine for me
http://dustyreagan.com/downgrade-phpunit-3-6-to-3-5-15/
install it via composer:
{
...
"repositories": [
{
"type": "pear",
"url": "pear.symfony-project.com"
},
{
"type": "pear",
"url": "pear.phpunit.de"
}
],
"require-dev": {
"pear-pear.phpunit.de/phpunit": "3.5.15",
"pear-pear.phpunit.de/PHP_CodeCoverage": "1.0.*",
"pear-pear.phpunit.de/File_Iterator": "1.2.3"
}
}