R package installation with GitHub - github

I am trying to install the package "PITE" as it is mentioned in the codes used in the article "Subgroup Identification Clinical Trials via the Predicted Individual Treatment Effect". The codes are taken from "https://github.com/nicoballarini/PLOS-2018-PITE#subgroup-identification-clinical-trials-via-the-predicted-individual-treatment-effect". But I'm unable to load this package, it would be very helpful if anyone can tell me where am I going wrong? The error message that I get:
install_github("nicoballarini/PLOS-2018-PITE")
Downloading GitHub repo nicoballarini/PLOS-2018-PITE#master
✓ checking for file ‘/private/var/folders/ml/wj8v_nld19n52l2g3tvzmltr0000gn/T/RtmpD4r8z6/remotes186f6614c26d/nicoballarini-PLOS-2018-PITE-832e47b/DESCRIPTION’ ...
─ preparing ‘PITE’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘PITE_0.1.0.tar.gz’
* installing *source* package ‘PITE’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘broom’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/libs/Rcpp.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/libs/Rcpp.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/libs/Rcpp.so
Reason: image not found
Error: package ‘broom’ could not be loaded
Execution halted
ERROR: lazy loading failed for package ‘PITE’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/PITE’
Error: Failed to install 'PITE' from GitHub:
(converted from warning) installation of package ‘/var/folders/ml/wj8v_nld19n52l2g3tvzmltr0000gn/T//RtmpD4r8z6/file186f5ce8b676/PITE_0.1.0.tar.gz’ had non-zero exit status
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/libs/Rcpp.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/libs/Rcpp.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/libs/Rcpp.so
Reason: image not found

Related

Swift Package Manager failed extracting

I'm getting this Package Manager error, when switching to a different branch or cloning the project. Build fails and "Clean Build Folder" doesn't help.
Error:
failed extracting
'https://releases.amplify.aws/aws-sdk-ios/AWSConnect-2.26.6.zip'
which is required by binary target 'AWSConnect':
.../Library/Developer/Xcode/DerivedData/MyApp-cbgtlihuudupsqdzyjdbyvcwkilh/SourcePackages/artifacts/extract/AWSConnect
is not a directory
The following steps resolve the issue forcing all packages to download.
Product > Clean Build Folder
Delete DerivedData content (Preferences > Locations > Derived Data little arrow)
File > Packages > Reset Package Cache
Build
The Reset Package Cache step is the most important here. It forces all packages to download as if they where just added.
Another issue that can happen is if you have added a build configuration, make sure that you have replicated this build configuration name throughout all your in house libraries, frameworks and sub projects. If the project that uses your Library has no build configuration for the scheme you are building then it will not link and you will receive errors like:
failed extracting 'https://github.com/*.xcframework.zip' which is required by binary target 'BlahBlah': fchmod (file attributes) error: Operation not permitted

When I try to upload my package to PyPI why do I get an upload failed?

The upload failed and I see there is a warning that MANIFEST.in does not exist and standard file not found: should have one of README, README.txt, README.rst.
Can someone please help? I'm not sure if I need to create the manifest template and standard readme files or if there's something wrong with the code I'm using:
C:\Users\Sean\Desktop\Projects\Head_First_Python\nester>python setup.py sdist upload
running sdist
running check
warning: sdist: manifest template 'MANIFEST.in' does not exist (using default file list)
warning: sdist: standard file not found: should have one of README, README.txt, README.rst
writing manifest file 'MANIFEST'
creating nester-1.0.0
making hard links in nester-1.0.0...
hard linking nester.py -> nester-1.0.0
hard linking setup.py -> nester-1.0.0
Creating tar archive
removing 'nester-1.0.0' (and everything under it)
running upload
Submitting dist\nester-1.0.0.tar.gz to https://upload.pypi.org/legacy/
Upload failed (403): Invalid or non-existent authentication information. See https://pypi.org/help/#invalid-auth for details
error: Upload failed (403): Invalid or non-existent authentication information. See https://pypi.org/help/#invalid-auth for details
C:\Users\Sean\Desktop\Projects\Head_First_Python\nester>

bitbake recipe compiles but cannot be included into image

I have a recipe that compiles C code and I have a python recipe that depends on that C library. Both can be bitbaked and when I scrutinize the environment of the python recipe the C library shows up as expected. I also have an image recipe that adds the python recipe as IMAGE_INSTALL. When I check the dependency graph all dependencies seem to be resolved just fine. Nevertheless, compilation fails:
DNF version: 4.1.0
cachedir: /home/marius/mender-orangepi-warrior/build/tmp/work/orange_pi_zero-poky-linux-gnueabi/quakesaver-image/1.0-r0/rootfs/var/cache/dnf
Added oe-repo repo from /home/marius/mender-orangepi-warrior/build/tmp/work/orange_pi_zero-poky-linux-gnueabi/quakesaver-image/1.0-r0/oe-rootfs-repo
repo: using cache for: oe-repo
not found other for:
not found modules for:
not found deltainfo for:
not found updateinfo for:
oe-repo: using metadata from Fri 27 Mar 2020 11:40:54 AM UTC.
Last metadata expiration check: 0:00:01 ago on Fri 27 Mar 2020 11:40:54 AM UTC.
No module defaults found
No match for argument: wiringop
Error: Unable to find a match
ERROR: quakesaver-image-1.0-r0 do_rootfs:
ERROR: quakesaver-image-1.0-r0 do_rootfs: Function failed: do_rootfs
ERROR: Logfile of failure stored in: /home/marius/mender-orangepi-warrior/build/tmp/work/orange_pi_zero-poky-linux-gnueabi/quakesaver-image/1.0-r0/temp/log.do_rootfs.20584
ERROR: Task (/home/marius/mender-orangepi-warrior/build/../sources/meta-quakesaver/recipes-core/images/quakesaver-image.bb:do_rootfs) failed with exit code '1'
Any hints, how to further investigate this issue? As I said, both dependencies are properly resolved in the graph. Strange...
I mistakenly had the C dependency added to the python runtime dependencies (RDEPENDS_${PN}) which, of course, is nonsense.

Raspberry Pi 4 yocto, rpi-basic-image.bb: Unable to determine endianness for architecture 'INVALID'

I'm trying to build core-image-minimal for raspberrypi4-64 on the zeus branch
and I had to create the file sanity.conf and I'm getting this errors:
fstrati$ bitbake -c cleanall core-image-minimal
Loading cache: 100% Time: 0:00:00
Loaded 28 entries from dependency cache.
ERROR: rpi-basic-image.bb: Unable to determine endianness for architecture 'INVALID'
ERROR: rpi-basic-image.bb: Please add your architecture to siteinfo.bbclass
ERROR: rpi-hwup-image.bb: Unable to determine endianness for architecture 'INVALID'
ERROR: rpi-hwup-image.bb: Please add your architecture to siteinfo.bbclass
ERROR: Failed to parse recipe: rpi-hwup-image.bb
ERROR: vte_0.56.3.bb: Unable to determine endianness for architecture 'INVALID'
ERROR: vte_0.56.3.bb: Please add your architecture to siteinfo.bbclass
I don't understand why core-image-minimal is using such deprecated recipes.
do I need to switch to the master branch?
Forgive me if this is a dumb question...
It seems my MACHINE configuration was wrong. I tried with MACHINE ?= "raspberrypi4-64" instead and everything went fine.
Removing conf resolved issue for me as well.

Unable to load resource for composite template

I have a very basic GTK application written in Vala (non-working source tree here), which intend to load the resources for the main application window from a GResource.
So I created a resource file, compiled it with glib-compile-resources and also added it to VALAFLAGS as --gresources=$(top_srcdir)/data/gauthenticator.gresource.xml.
The relevant part of the data file looks like this:
<gresource prefix="/eu/polonkai/gergely/gauthenticator">
<file preprocess="xml-stripblanks">gauth-window.ui</file>
</gresource>
and I use it like this:
[GtkTemplate (ui = "/eu/polonkai/gergely/gauthenticator/gauth-window.ui")]
class Window : Gtk.ApplicationWindow {
[GtkChild]
private Gtk.ProgressBar countdown;
}
The relevant part of my Makefile.am:
gresource_file = $(top_srcdir)/data/gauthenticator.gresource.xml
gauthenticator_VALAFLAGS = --pkg gtk+-3.0 --target-glib=2.38 --gresources $(gresource_file)
All is well during compilation, but in runtime I get this error:
(gauthenticator:16501): Gtk-CRITICAL **: Unable to load resource for composite template for type 'GAuthenticatorWindow': The resource at '/eu/polonkai/gergely/gauthenticator/gauth-window.ui' does not exist
(gauthenticator:16501): Gtk-CRITICAL **: gtk_widget_class_bind_template_child_full: assertion 'widget_class->priv->template != NULL' failed
(gauthenticator:16501): Gtk-CRITICAL **: gtk_widget_init_template: assertion 'template != NULL' failed
I copied most resource-related lines from the GNOME Boxes repository, but obviously missed something.
How are you compiling the resources with glib-compile-resources? I would recommend compiling it to a C file:
glib-compile-resources --sourcedir data --generate-source --target my_build_dir/resources/resources.c data/gauthenticator.gresource.xml
Then add my_build_dir/resources/resources.c to your _SOURCES so it gets compiled along with your Vala sources. The --gresources option for valac only does type checking for Vala's GTK+ composite template support.
I've not tried compiling a GResource C file as part of a Vala to C and then C to binary compilation process. At the moment it looks like you are just using valac for the whole compilation process.