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.
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 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!
I am not able to connect to JIRA using R. Following are the details which might help you to help me.
R version being used:
R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
Installed package RJDBC. I get following output after loading the library
library('RJDBC')
Loading required package: DBI
Loading required package: rJava
Warning messages:
1: package ‘RJDBC’ was built under R version 3.4.4
2: package ‘DBI’ was built under R version 3.4.4
3: package ‘rJava’ was built under R version 3.4.3
Installed and loaded cdata
library('cdata')
Loading required package: wrapr
Warning messages:
1: package ‘cdata’ was built under R version 3.4.4
2: package ‘wrapr’ was built under R version 3.4.4
How do I remove below error?
driver <- JDBC(driverClass = "cdata.jdbc.jira.JiraDriver", classPath = "MyInstallationDir//lib//cdata.jdbc.jira.jar", identifier.quote = "'")
Error in .jfindClass(as.character(driverClass)[1]) : class not found
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007ff17a60c678, pid=4219, tid=140673779791616
#
# JRE version: Java(TM) SE Runtime Environment (8.0-b124) (build 1.8.0-ea-b124)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.0-b66 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# V [libjvm.so+0x665678] jni_invoke_nonstatic(JNIEnv_*, JavaValue*, _jobject*, JNICallType, _jmethodID*, JNI_ArgumentPusher*, Thread*)+0x38
#
# 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:
# /media/data/K's World/javaFX/ChatApp/hs_err_pid4219.log
Compiled method (c1) 16675 988 3 java.util.concurrent.atomic.AtomicBoolean::set (14 bytes)
total in heap [0x00007ff16535ef50,0x00007ff16535f2a0] = 848
relocation [0x00007ff16535f070,0x00007ff16535f0a0] = 48
main code [0x00007ff16535f0a0,0x00007ff16535f1c0] = 288
stub code [0x00007ff16535f1c0,0x00007ff16535f250] = 144
metadata [0x00007ff16535f250,0x00007ff16535f258] = 8
scopes data [0x00007ff16535f258,0x00007ff16535f268] = 16
scopes pcs [0x00007ff16535f268,0x00007ff16535f298] = 48
dependencies [0x00007ff16535f298,0x00007ff16535f2a0] = 8
#
# If you would like to submit a bug report, please visit:
# http://bugreport.sun.com/bugreport/crash.jsp
#
I am writing chat App in javaFx..and I am using eclipse IDE..
My Application is running well but I don't know why suddenly application has been stopped.
It sounds like you're running JavaFX with Java 8 on Linux, and you've run into this bug:
https://bugs.openjdk.java.net/browse/JDK-8141687
App crashes while starting Main.class in JavaFx
ava version "1.8.0_60" Java(TM) SE Runtime Environment (build
1.8.0_60-b27) Java HotSpot(TM) 64-Bit Server VM (build 25.60-b23, mixed mode)
ADDITIONAL OS VERSION INFORMATION : Mint17.2 Cinnamon 64Bit
SUGGESTION: Try a different version of Java/JavaFX.
Run sudo update-alternatives --config java to see what alternatives are already present on your system. I would downgrade to Java 1.7 if possible.
https://askubuntu.com/questions/272187/setting-jdk-7-as-default
If there are no suitable candidates, use apt-get install openjdk-7-jdk:
https://www.digitalocean.com/community/tutorials/how-to-install-java-on-ubuntu-with-apt-get
I had the same issue (except that it was java-8-oracle build 101) and found out why it was happening:
I have a login screen that appears before my main application and that screen gets closed after the login occurs and, apparently, closing it (or even hiding it) and showing a new window makes it crash.