I am writing a function that i want to include in a user-defined package (MYPACKAGE). The function is a follows:
readSchedule <- function(FILE){
WB = loadWorkbook(FILE)
WS= readWorksheet(WB, sheet = 'Sheet1',header = TRUE)
return(WS)
}
where FILE is the name of the Excel file i want to read. When writing this function, I want it to import XLConnect, since that is the package it uses. I placed header code defining the function:
#param FILE Excel file
#return Excel data
#export
#import XLConnect
I have also added import(XLConnect) to the NAMESPACE and the DESCRIPTION file of MYPACKAGE. The package builds fine (or at least at first cut it appears to build OK) but when i run "Check Package" it fails and gives me the following error:
* installing *source* package 'MYPACKAGE' ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: fun(libname, pkgname)
error: No CurrentVersion entry in Software/JavaSoft registry! Try re-installing Java and make sure R and Java have matching architectures.
Error: loading failed
Execution halted
*** arch - x64
ERROR: loading failed for 'i386'
I have the correct version of Java and can load rJava just fine. i've tried importing rJava (similar to XLConnect) but i get the same error. Below is my sessionInfo:
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] MYPACKAGE
loaded via a namespace (and not attached):
[1] chron_2.3-45 data.table_1.9.4 digest_0.6.8 lubridate_1.3.3 memoise_0.2.1 plyr_1.8.1
[7] Rcpp_0.11.1 reshape2_1.4 rJava_0.9-6 stringr_0.6.2 tools_3.1.2 XLConnect_0.2-7
It looks like you are building your package on a Windows 64-bit machine with a 64-bit version of Java installed. When checking your package using R CMD check, R by default also attempts to check your package on other sub-architectures (i386, 32-bit) which in your case would in addition require a 32-bit installation of Java.
If you want to check your package also for i386 you may just additionally install Java 32-bit. The other option is to pass the option --no-multiarch to your R CMD check call, e.g. R CMD check --no-multiarch MYPACKAGE.
Related
After booting SWUpdate yocto-generated image for the first time, executing swupdate results in error message:
Error parsing configuration file: 'globals' section missing, exiting.
I tried to strictly follow SWUpdate's documentation, but it gets short when it comes to yocto integration. I'm using meta-swupdate, meta-swupdate-boards, and meta-openembedded layers together with poky example repository all at Kirkstone tag, building via bitbake update-image and having modyfied local.conf as:
MACHINE ??= "raspberrypi4-64"
ENABLE_UART = "1"
RPI_USE_U_BOOT = "1"
IMAGE_FSTYPES = "wic ext4.gz"
PREFERRED_PROVIDER_u-boot-fw-utils = "libubootenv"
IMAGE_INSTALL:append = " swupdate"
Is there anything else I need to modify to generate the configuration file and be able to run SWUpdate binary properly?
Side question: In the documentation, it's recommended to append swupdate-www to achieve a better web server. However, if I append it, there is no swupdate-www binary inside the `/usr/bin' directory.
As with other recipes folders the recipes-support/swupdate/swupdate/raspberrypi4-64 folder was missing inside the meta-swupdate-boards layer. Therefore, an empty config file was always generated. After adding this folder and all related files, strongly inspired by raspberrypi3 folder, the error was gone and swupdate -h provided the expected output.
There was also one new error during build process thrown by yocto. It was related to missing systemd requirement and was solved by adding:
DISTRO_FEATURES_append = " systemd"
to local.conf
When I try to install tmap:
install.packages("tmap")
I have the following mistake:
also installing the dependencies ‘tmaptools’, ‘sf’
There are binary versions available but the source versions are later:
binary source needs_compilation
sf 0.9-0 0.9-2 TRUE
tmap 2.3-2 3.0 FALSE
Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/tmaptools_3.0.zip'
Content type 'application/zip' length 178880 bytes (174 KB)
downloaded 174 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/sf_0.9-0.zip'
Content type 'application/zip' length 39675549 bytes (37.8 MB)
downloaded 37.8 MB
package ‘tmaptools’ successfully unpacked and MD5 sums checked
package ‘sf’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Marine\AppData\Local\Temp\RtmpSQF9EP\downloaded_packages
installing the source package ‘tmap’
trying URL 'https://cran.rstudio.com/src/contrib/tmap_3.0.tar.gz'
Content type 'application/x-gzip' length 2936348 bytes (2.8 MB)
downloaded 2.8 MB
* installing *source* package 'tmap' ...
** package 'tmap' correctement décompressé et sommes MD5 vérifiées
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace 'sf' 0.9-0 is being loaded, but = 0.9.1 is required
Calls: <Anonymous ... withCallingHandlers - loadNamespace - namespaceImport - loadNamespace
Exécution arrêtée
ERROR: lazy loading failed for package 'tmap'
* removing 'C:/Program Files/R/R-3.6.3/library/tmap'
Warning in install.packages :
installation of package ‘tmap’ had non-zero exit status
So I guess this is a problem with the sf version, but when I try to install sf independently, it is the version 0.9-0. that I install, and I cannot install 0.9.1 or more as required.
Any tip to overcome this issue?
Thanks!
PS: I use R version 3.6.3
When I try to install multiples packages with a wildcard naming I got the following error:
* yum_package[mysql-server] action install (up to date)
* yum_package[mysql*] action install
* No candidate version available for mysql*
============================================================================ ====
Error executing action `install` on resource 'yum_package[mysql*]'
============================================================================ ====
Recipe code is:
package 'mysql-server' do
action :install
end
package 'mysql*' do
action :install
end
You have to use the exact package name. The chef package resource does no magic to find matching packages.
The name of the resource (the part just after package) is used as the package name and given to the underlying system (yum on RH like systems, apt on debian like systems)
If you have multiples packages to install and a common configuration you can loop over them in your recipe instead:
['mysql-server','mysql-common','mysql-client'].each do |p|
package p do
action :install
end
end
The array creation could be simplified with some ruby syntax as the words builder %w:
%w(mysql-server mysql-common mysql-client).each [...]
Since chef 12.1 the package resource accept an array of packages directly like this:
package %w(mysql-server mysql-common mysql-client)
This can be resolved using chef cases. Please see below
add the following to your attributes file:
packages = []
case node[:platform_family]
when 'rhel' #based on your OS
packages = [
"package1",
"package2",
"package3",
"package4",
"package5",
"package6",
"package7" ## Last line without comma
]
end
default[:cookbookname][:packages] = packages
Then, add the following to your recipe file (recipes/default.rb):
node[:cookbookname][:packages].each do |pkg|
package pkg do
action :install
retries 3
retry_delay 5
end
end
Running chef-solo (Installing Chef Omnibus (12.3)) on centos6.6
My recipe has the following simple code:
package 'cloud-init' do
action :install
end
log 'rpm-qi' do
message `rpm -qi cloud-init`
level :warn
end
log 'yum list' do
message `yum list cloud-init`
level :warn
end
But it outputs the following:
- install version 0.7.5-10.el6.centos.2 of package cloud-init
* log[rpm-qi] action write[2015-07-16T16:46:35+00:00] WARN: package cloud-init is not installed
[2015-07-16T16:46:35+00:00] WARN: Loaded plugins: fastestmirror, presto
Available Packages
cloud-init.x86_64 0.7.5-10.el6.centos.2 extras
I am at a loss as to why rpm/yum and actually rpmquery don't see the package as installed.
EDIT: To clarify I am specifically looking for the following string post package install to then apply a change to the file (I understand this is not a very chef way to do something I am happy to accept suggestions):
rpmquery -l cloud-init | grep 'distros/__init__.py$'
I have found that by using the following:
install_report = shell_out('yum install -y cloud-init').stdout
cloudinit_source = shell_out("rpmquery -l cloud-init | grep 'distros/__init__.py$'").stdout
I can then get the file I am looking for and perform
Chef::Util::FileEdit.new(cloudinit_source.chomp(''))
The file moves based on the distribution but I need to edit that file specifically with in place changes.
Untested code, just to give the idea:
package 'cloud-init' do
action :install
notifies :run,"ruby_block[update_cloud_init]"
end
ruby_block 'update_cloud_init' do
block do
cloudinit_source = shell_out("rpmquery -l cloud-init | grep 'distros/__init__.py$'").stdout
rc = Chef::Util::FileEdit.new(cloudinit_source.chomp(''))
rc.search_file_replace_line(/^what to find$/,
"replacement datas for the line")
rc.write_file
end
end
ruby_block example taken and adapted from here
I would better go using a template to manage the whole file, what I don't understand is why you don't know where it will be at first...
Previous answer
I assume it's a compile vs converge problem. at the time the message is stored (and so your command is executed) the package is not already installed.
Chef run in two phase, compile then converge.
At compile time it build a collection of resources and at converge time it execute code for the resource to get them in the described state.
When your log resource is compiled, the ugly back-ticks are evaluated, at this time there's a package resource in the collection but the resource has not been executed, so the output is correct.
I don't understand what you want to achieve with those log resources at all.
If you want to test your node state after chef-run use a handler maybe calling ServerSpec as in Test-Kitchen.
I've seen many questions in this forum which are questions of how to fix a problems of compiling IronPython WPF to exe.
But the problem is that I haven't seen any guide Step-by-step of how to compile my project.
I understood it includes using the clr module.
I've 6 files:
Window.py, Window.xaml.
Window1.py, Window1.xaml.
Window2.py, Window2.xaml.
That's all the files
Thanks
((irrelevant: Update- 3 hours later:
I've started using SharpDevelop and when I run it through the software itself it can be run. However , when I try to run this through the .exe file in the project's folder it doesn't work... ))
Update 2 - SharpDevelop created an exe file which works but the problem is it didn't encrypt my xaml to dll ..
Have you tried the script from this thread: Ironpython 2.6 .py -> .exe
Supposedly it includes wpf support:
#!/usr/bin/env python
# CompileToStandalone, a Python to .NET ILR compiler which produces standalone binaries
# (C) 2012 Niall Douglas http://www.nedproductions.biz/
# Created: March 2012
import modulefinder, sys, os, subprocess, _winreg
if len(sys.argv)<2:
print("Usage: CompileEverythingToILR.py <source py> [-outdir=<dest dir>]")
sys.exit(0)
if sys.platform=="cli":
print("ERROR: IronPython's ModuleFinder currently doesn't work, so run me under CPython please")
sys.exit(1)
sourcepath=sys.argv[1]
destpath=sys.argv[2][8:] if len(sys.argv)==3 else os.path.dirname(sys.argv[0])
ironpythonpath=None
try:
try:
keyh=_winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE, "SOFTWARE\\IronPython\\2.7\\InstallPath")
ironpythonpath=_winreg.QueryValue(keyh, None)
except Exception as e:
try:
keyh=_winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE, "SOFTWARE\\Wow6432Node\\IronPython\\2.7\\InstallPath")
ironpythonpath=_winreg.QueryValue(keyh, "")
except Exception as e:
pass
finally:
if ironpythonpath is not None:
_winreg.CloseKey(keyh)
print("IronPython found at "+ironpythonpath)
else:
raise Exception("Cannot find IronPython in the registry")
# What we do now is to load the python source but against the customised IronPython runtime
# library which has been hacked to work with IronPython. This spits out the right set of
# modules mostly, but we include the main python's site-packages in order to resolve any
# third party packages
print("Scanning '"+sourcepath+"' for dependencies and outputting into '"+destpath+"' ...")
searchpaths=[".", ironpythonpath+os.sep+"Lib"]
searchpaths+=[x for x in sys.path if 'site-packages' in x]
finder=modulefinder.ModuleFinder(searchpaths)
finder.run_script(sourcepath)
print(finder.report())
modules=[]
badmodules=finder.badmodules.keys()
for name, mod in finder.modules.iteritems():
path=mod.__file__
# Ignore internal modules
if path is None: continue
# Ignore DLL internal modules
#if '\\DLLs\\' in path: continue
# Watch out for C modules
if os.path.splitext(path)[1]=='.pyd':
print("WARNING: I don't support handling C modules at '"+path+"'")
badmodules.append(name)
continue
modules.append((name, os.path.abspath(path)))
modules.sort()
print("Modules not imported due to not found, error or being a C module:")
print("\n".join(badmodules))
raw_input("\nPress Return if you are happy with these missing modules ...")
with open(destpath+os.sep+"files.txt", "w") as oh:
oh.writelines([x[1]+'\n' for x in modules])
cmd='ipy64 '+destpath+os.sep+'pyc.py /main:"'+os.path.abspath(sourcepath)+'" /out:'+os.path.splitext(os.path.basename(sourcepath))[0]+' /target:exe /standalone /platform:x86 /files:'+destpath+os.sep+'files.txt'
print(cmd)
cwd=os.getcwd()
try:
os.chdir(destpath)
retcode=subprocess.call(cmd, shell=True)
finally:
os.chdir(cwd)
sys.exit(retcode)