I have an embarrassing error when deploy a simple app to shinyapps.io.
The app needs only one more package "Seurat" which I load in server.R by library(Seurat). But When I deploy it to shinyappsio.io, it stopped and showed:
Preparing to deploy application...DONE
Uploading bundle for application: 1762339...DONE
Deploying bundle: 2806268 for application: 1762339 ...
Waiting for task: 693229180
building: Processing bundle: 2806268
building: Parsing manifest
################################ Begin Task Log ################################
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 693229181 failed: Error parsing manifest: Unable to determine package source for Bioconductor package Biobase: Repository must be specified
Execution halted
While it seems to be a simple repository specification problem. So I tried changing the repos:
options(repos = BiocManager::repositories())
which didn't help, then I tried:
setRepositories()
and choose the "BioC software" and it doesn't help either. The error specified for the Bioconductor package Seurat:
Preparing to deploy application...DONE
Uploading bundle for application: 1762339...DONE
Deploying bundle: 2806287 for application: 1762339 ...
Waiting for task: 693231225
building: Processing bundle: 2806287
building: Parsing manifest
################################ Begin Task Log ################################
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 693231227 failed: Error parsing manifest: Unable to determine package source for Bioconductor package Seurat: Repository must be specified
Execution halted
Then I found Seurat is even not a bioconductor package and should be found with r CRAN:
https://cran.r-project.org/web/packages/Seurat/index.html
I have no other solution in my head. Could anyone help me out? Thank you!
Here's current options("repos"):
> options("repos")
$repos
CRAN
"https://cloud.r-project.org"
BioCsoft
"https://bioconductor.org/packages/3.10/bioc"
BioCann
"https://bioconductor.org/packages/3.10/data/annotation"
BioCexp
"https://bioconductor.org/packages/3.10/data/experiment"
Here's my sessioninfo:
R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_3.2.1 Seurat_3.1.3 shiny_1.4.0
loaded via a namespace (and not attached):
[1] TH.data_1.0-10 Rtsne_0.15 colorspace_1.4-1 ggridges_0.5.2 rsconnect_0.8.16 rstudioapi_0.11
[7] leiden_0.3.3 listenv_0.8.0 npsurv_0.4-0 ggrepel_0.8.1 mvtnorm_1.0-12 codetools_0.2-16
[13] splines_3.6.2 mnormt_1.5-6 lsei_1.2-0 TFisher_0.2.0 jsonlite_1.6.1 packrat_0.5.0
[19] ica_1.0-2 cluster_2.1.0 png_0.1-7 uwot_0.1.5 sctransform_0.2.1 BiocManager_1.30.10
[25] compiler_3.6.2 httr_1.4.1 assertthat_0.2.1 Matrix_1.2-18 fastmap_1.0.1 lazyeval_0.2.2
[31] later_1.0.0 htmltools_0.4.0 tools_3.6.2 rsvd_1.0.2 igraph_1.2.4.2 gtable_0.3.0
[37] glue_1.3.1 RANN_2.6.1 reshape2_1.4.3 dplyr_0.8.4 rappdirs_0.3.1 Rcpp_1.0.3
[43] Biobase_2.46.0 vctrs_0.2.2 multtest_2.42.0 gdata_2.18.0 ape_5.3 nlme_3.1-144
[49] gbRd_0.4-11 lmtest_0.9-37 stringr_1.4.0 globals_0.12.5 mime_0.9 lifecycle_0.1.0
[55] irlba_2.3.3 gtools_3.8.1 future_1.16.0 MASS_7.3-51.5 zoo_1.8-7 scales_1.1.0
[61] promises_1.1.0 parallel_3.6.2 sandwich_2.5-1 RColorBrewer_1.1-2 curl_4.3 reticulate_1.14
[67] pbapply_1.4-2 gridExtra_2.3 stringi_1.4.5 mutoss_0.1-12 plotrix_3.7-7 caTools_1.18.0
[73] BiocGenerics_0.32.0 bibtex_0.4.2.2 Rdpack_0.11-1 rlang_0.4.4 pkgconfig_2.0.3 bitops_1.0-6
[79] lattice_0.20-38 ROCR_1.0-7 purrr_0.3.3 htmlwidgets_1.5.1 cowplot_1.0.0 tidyselect_1.0.0
[85] RcppAnnoy_0.0.14 plyr_1.8.5 magrittr_1.5 R6_2.4.1 gplots_3.0.1.2 multcomp_1.4-12
[91] withr_2.1.2 pillar_1.4.3 sn_1.5-5 fitdistrplus_1.0-14 survival_3.1-8 tibble_2.1.3
[97] future.apply_1.4.0 tsne_0.1-3 crayon_1.3.4 KernSmooth_2.23-16 plotly_4.9.2 grid_3.6.2
[103] data.table_1.12.8 metap_1.3 digest_0.6.24 xtable_1.8-4 tidyr_1.0.2 httpuv_1.5.2
[109] numDeriv_2016.8-1.1 openssl_1.4.1 RcppParallel_4.4.4 stats4_3.6.2 munsell_0.5.0 viridisLite_0.3.0
[115] askpass_1.1
I had this exact problem, but after many many hours I found the solution in this thread:
https://github.com/satijalab/seurat/issues/2716
You simply need to install the development version. Hope this helps!
Related
I am for the first time trying to make a website with blogdown. On running
setwd("..to-my-empty-website-directory..")
library(blogdown)
new_site(theme="yihui/hugo-xmin", dir=".")
I get the error
> new_site(theme="yihui/hugo-xmin", dir=".")
― Creating your new site
| Installing the theme yihui/hugo-xmin from github.com
trying URL 'https://github.com/yihui/hugo-xmin/archive/HEAD.tar.gz'
downloaded 68 KB
Error in dir.exists(x) : invalid filename argument
What is wrong? I have latest versions of hugo v0.103.0 and RStudio 2022.07.1 Build 554. All R packages are up-to-date. Here is Session info
> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.7
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] blogdown_1.12.1
loaded via a namespace (and not attached):
[1] compiler_4.2.1 tools_4.2.1 yaml_2.3.5 knitr_1.40 xfun_0.33
This is a bug in blogdown, and I have just fixed it in the dev version. Please try the dev version:
remotes::install_github('rstudio/blogdown')
I'm using Julia 1.5.3 and last versions of module DataFrames.jl (v0.22.0) and Compat.jl (v3.23.0).
I've added DataFrames into my project enviroment as usual:
]add DataFrames
Last time I've used DataFrames package in July 2020.
Now when i'm trying to use (call using DataFrames) the package I have an error:
[ Info: Precompiling DataFrames [a93c6f00-e57d-5684-b7b6-d8193f3e46c0]
ERROR: LoadError: LoadError: UndefVarError: ComposedFunction not defined
Stacktrace:
[1] top-level scope at C:\Users\yzh\.julia\packages\DataFrames\X0xNW\src\other\utils.jl:82
[2] include(::Function, ::Module, ::String) at .\Base.jl:380
[3] include at .\Base.jl:368 [inlined]
[4] include(::String) at C:\Users\yzh\.julia\packages\DataFrames\X0xNW\src\DataFrames.jl:1
[5] top-level scope at C:\Users\yzh\.julia\packages\DataFrames\X0xNW\src\DataFrames.jl:94
[6] include(::Function, ::Module, ::String) at .\Base.jl:380
[7] include(::Module, ::String) at .\Base.jl:368
[8] top-level scope at none:2
[9] eval at .\boot.jl:331 [inlined]
[10] eval(::Expr) at .\client.jl:467
[11] top-level scope at .\none:3
in expression starting at C:\Users\yzh\.julia\packages\DataFrames\X0xNW\src\other\utils.jl:79
in expression starting at C:\Users\yzh\.julia\packages\DataFrames\X0xNW\src\DataFrames.jl:94
But tests Pkg.test("DataFrames") have passed corretly without an errors!
I think I have some troubles with the Compat - package. When I'm trying to export ComposedFunction separetly:
using Compat: ComposedFunction
I also have an error:
UndefVarError: ComposedFunction not defined
in include_string at base\loading.jl:1088
I've tried several things:
remove the packages and install again;
]up
Pkg.resolve
update Julia from 1.5.2 to 1.5.3
restart computer, of course
delete all folders besides "dev" and "environment" from .julia directory
but the errors still exist.
Thanks for your help.
I've re-run Atom again in administrator mode and all errors disappeared. Now everything works without admin mode also. Magic.
I am trying to setup Apache Atlas on my system. I am encountering the following error
I read the article as suggested (http://cwiki.apache.org/confluence/display/MAVEN/PluginConfigurationException) but I was unable to understand what it was trying to convey.
[INFO] >>> findbugs-maven-plugin:3.0.1:check (findbugs-check) > :findbugs # apache-atlas >>>
[INFO]
[INFO] --- findbugs-maven-plugin:3.0.1:findbugs (findbugs) # apache-atlas ---
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.codehaus.groovy.reflection.CachedClass$3$1 (file:/Users/r0r017e/.m2/repository/org/codehaus/groovy/groovy-all/2.4.0/groovy-all-2.4.0.jar) to method java.lang.Object.finalize()
WARNING: Please consider reporting this to the maintainers of org.codehaus.groovy.reflection.CachedClass$3$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
...
[INFO] Apache Atlas Server Build Tools 1.0 ................ SUCCESS [ 0.632 s]
[INFO] apache-atlas 1.1.0 ................................. FAILURE [ 3.341 s]
...
[ERROR] Failed to execute goal org.codehaus.mojo:findbugs-maven-plugin:3.0.1:findbugs (findbugs) on project apache-atlas: Unable to parse configuration of mojo org.codehaus.mojo:findbugs-maven-plugin:3.0.1:findbugs for parameter pluginArtifacts: Cannot assign configuration entry 'pluginArtifacts' with value '${plugin.artifacts}' of type java.util.Collections.UnmodifiableRandomAccessList to property of type java.util.ArrayList -> [Help 1]
I need to setup Apache Atlas via Cassandra as a backend store. I am new to data governance and open source solutions, any help would be appreciated!
If you are just testing Atlas I suggest using a docker image. The following worked for me. https://github.com/michalmiklas/atlas-docker
rxRemoteHadoopMRCall()
====== xxxx.cloudapp.azure.com (Master HPA Process) has started run at Sat Mar 18 08:15:43 2017 ======
17/03/18 03:16:36 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where application
Warning: libjvm.so not found in /log/cloudera/parcels/MRS-9.0.1/hadoop, searching system-wide
Internal Error: Cannot reset hdfs internal params while connected to an hdfs file system.
Error in try({ :
Internal Error: Cannot reset hdfs internal params while connected to an hdfs file system.
I wonder if this is a problem with locating JRE. You can try setting JAVA_HOME for your user ($HOME/.bashrc) or for all users (etc/environment) on the node you're connecting to. It should point to a place that correctly resolves this path: $JAVA_HOME/jre/lib/amd64/server/libjvm.so
I have been using SonarQube for code analyzing at a basic level however now I would like to measure the code against FX-COP rules. Hence I am attempting to use MSBuild SonarQube scanner. I read the documentation thoroughly and have setup my project likewise however when I execute it gives me error.
Below is the extract from the log:
MSBuild SonarQube Runner Bootstrapper 1.0.2.0
Default properties file was found at C:\....\1c36691bf5270463\SonarQube.Analysis.xml
Loading analysis properties from C:\....\1c36691bf5270463\SonarQube.Analysis.xml
Pre-processing started.
Preparing working directories...
Checking for updates...
MSBuild SonarQube Runner Pre-processor 1.0.2.0
Loading analysis properties from C:\...\1c36691bf5270463\SonarQube.Analysis.xml
Updating build integration targets...
Fetching analysis configuration settings...
Generating rulesets...
Pre-processing succeeded.
Microsoft (R) Build Engine version 12.0.21005.1
[Microsoft .NET Framework, version 4.0.30319.34209]
Copyright (C) Microsoft Corporation. All rights reserved.
Building the projects in this solution one at a time. To enable parallel build,
please add the "/m" switch.
Build started 11/20/2015 1:46:41 PM.
Project "C:\Project1.sln" on node 1 (rebuild target(s)).
ValidateSolutionConfiguration:
Building solution configuration "Debug|Any CPU".
Build succeeded.
9 Warning(s)
0 Error(s)
Time Elapsed 00:01:07.86
MSBuild SonarQube Runner Bootstrapper 1.0.2.0
Default properties file was found at C:\...\1c36691bf5270463\SonarQube.Analysis.xml
Loading analysis properties from C:\...\1c36691bf5270463\SonarQube.Analysis.xml
Post-processing started.
MSBuild SonarQube Runner Post-processor 1.0.2.0 gives several warnings similar to one below:
WARNING: File is not under the project directory and cannot currently be analysed
by SonarQube.
File: C:\Users\...\AppData\Local\Temp\2\.NETFramework,Version=v4.0.AssemblyAttributes.cs,
project: C:\...\1c36691bf5270463\SOURCE\x\y.csproj**
Calling the sonar-runner:
SONAR_RUNNER_OPTS is not configured. Setting it to the default value of -Xmx1024m
C:\...\1c36691bf5270463\.sonarqube\bin\sonar-runner\bin\..
SonarQube Runner 2.4
Java 1.8.0_51 Oracle Corporation (64-bit)
Windows Server 2008 R2 6.1 amd64
SONAR_RUNNER_OPTS=-Xmx1024m
INFO: Error stacktraces are turned on.
INFO: Runner configuration file: C:\...\1c36691bf5270463\.sonarqube\bin\sonar-runner\bin\..\conf\sonar-runner.properties
INFO: Project configuration file: C:\TeamCity\buildAgent\work\1c36691bf5270463\.sonarqube\out\sonar-project.properties
INFO: Default locale: "en_US", source code encoding: "UTF-8"
INFO: Work directory: C:\...\1c36691bf5270463\.sonarqube\out\.sonar
INFO: SonarQube Server 5.1.1
13:47:51.150 INFO - Load global repositories
13:47:51.743 INFO - Load global repositories (done) | time=593ms
13:47:51.758 INFO - Server id: 20151120125423
13:47:51.758 INFO - User cache: C:\...\cache
13:47:51.758 INFO - Install plugins
13:47:51.836 INFO - Install JDBC driver
.
.
.
13:47:55.518 INFO - ------------- Scan file1
13:47:55.534 INFO - Load module settings
13:47:55.658 INFO - Load rules
13:47:56.017 INFO - Base dir: C:\...\1c36691bf5270463\SOURCE\xxx
13:47:56.017 INFO - Working dir: C:\...\1c36691bf5270463\.sonarqube\out\.sonar\AC1_AC1_497EBFF2-C710-4843-8263-F534AF803D3E
13:47:56.017 INFO - Source encoding: UTF-8, default locale: en_US
13:47:56.532 INFO - Quality profile for cs: Sonar way
13:48:00.635 INFO - Sensor org.sonar.plugins.csharp.CSharpFxCopProvider$CSharpFxCopSensor#73c82ec1
INFO: -----------------------------------------------------------------
INFO: EXECUTION FAILURE
INFO: -----------------------------------------------------------------
Total time: 10.156s
Final Memory: 16M/306M
INFO: -----------------------------------------------------------------
13:48:00.791 Creating a summary markdown file...
Press any key to continue . . .
You need to run all your commands in a Developer Command Prompt for Visual Studio 2013 or higher and:
use at least MSBuild 12.0
have .NET 4.5.2+ installed
You have this error because the FxCop Results are not generated.
Do you see in the MSBuild's logs, execution of FxCop? This is visible inside the RunCodeAnalysis section of MSBuild's logs.
You need to run this from command line and use the "-X" flag on your command, this will give you verbose debugging, I would highly reccomend doing the following for troubleshooting.
sonar-runner.exe <arg> <arg> -X > sonar-runnerLog.txt
Then read or dump that log back here. either way you'll know a lot more about what the actual problem is.
You can get Visual Studio Express 2013 (or 15) for free and both of those come with their respective developer command prompts.