Error during precompiling DataFrames.jl: UndefVarError: ComposedFunction not defined - dataframe

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.

Related

blogdown::new_site(): Error in dir.exists(x) : invalid filename argument

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')

Unable to deploy app to shinyapps.io: Unable to determine package source

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!

How to install Apache Atlas 1.1.0 on MacOS Mojave?

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

SCIP JNI - JNIKnapsack example fails to run

I'm trying to use SCIP JNI using the SCIP Optimization Suite and compiling it from the source code using Ubuntu 16.04.
I compiled the jni interface folder, using the instructions provided in the site, but there seems to be an issue with the JniKnapsack example. When running it using the Makefile and the run.sh available in the folder:
make run
The output is:
SCIP version 3.2.1 [precision: 8 byte] [memory: block] [mode: optimized] [LP solver: SoPlex 2.2.1] [GitHash: c7c6c02]
Copyright (c) 2002-2016 Konrad-Zuse-Zentrum fuer Informationstechnik Berlin (ZIB)
created variables <x0>
variables pointer <1958512920>
created variables <x1>
variables pointer <1958513276>
created variables <x2>
variables pointer <1958517056>
created variables <x3>
variables pointer <1958517412>
created variables <x4>
variables pointer <1958517768>
created variables <x5>
variables pointer <1958518124>
created variables <x6>
variables pointer <1958521568>
created variables <x7>
variables pointer <1958521924>
created variables <x8>
variables pointer <1958522280>
created variables <x9>
variables pointer <1958522636>
*** 10.0
*** 11.0
*** 12.0
*** 13.0
*** 14.0
*** 15.0
*** 16.0
*** 17.0
*** 18.0
*** 19.0
*** 11
*** Value found: -1.0
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x74823c65, pid=18485, tid=3057216320
#
# JRE version: OpenJDK Runtime Environment (8.0_91-b14) (build 1.8.0_91-8u91-b14-0ubuntu4~16.04.1-b14)
# Java VM: OpenJDK Server VM (25.91-b14 mixed mode linux-x86 )
# Problematic frame:
# C [libscip.linux.x86.gnu.opt.so+0x44bc65] SCIPsolGetVal+0x35
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /home/david/workspace/scipoptsuite-3.2.1/scip-3.2.1/interfaces/jni/examples/JniKnapsack/hs_err_pid18485.log
#
# If you would like to submit a bug report, please visit:
# http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

Error: could not find function "sqldf" using R to run SQL

I faced a question,there is a error message to run sqldf package. I just load
install.packages("sqldf")
install.packages("RSQLite")
install.packages("tcltk2")
library("sqldf")
library("RSQLite")
library("tcltk2")
final <-sqldf("select a.age,
a.height
from a
inner join b
on
a.id = b.id
")
Error: could not find function "sqldf"
sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] tcltk stats graphics grDevices utils datasets methods base
other attached packages:
[1] tcltk2_1.2-11
loaded via a namespace (and not attached):
[1] tools_3.2.0
Also, my R and Rstudio have latest version. I have Windows 7.