I have a headache and want to crack. Loading the same package will report different errors every time

Because the paint on the front MAC keyboard fell off and the tab key failed, the new semester student discount began, so I changed a new Mac by the way. After configuring the environment, something very strange happened. It has been tossing around for two or three days. It's worth sharing:

Generally speaking, when you get a brand-new computer, install R and rstudio and the corresponding R package according to the bioinformatics office computer environment configuration tutorial I wrote five years ago. See the following for details: http://www.bio-info-trainee.com/3727.html

However, when loading the package, there are error reports that I can't understand. Every time I need to reopen rstudio and then load library(RTN). Can you see several different error reports below?

*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
 error: package or namespace load failed for 'RTN' in is(fdef, "groupGenericFunction"):
 Object not found'object'
 error: package or namespace load failed for 'RTN' in assign(.sigLabel(sig), el, envir = table):
 The first parameter is incorrect
> library(RTN)
error: package or namespace load failed for 'RTN' in .getGeneric(f, where, package):
 'The argument "f" to getGeneric'Must be a single string(Now it is classified as"call"Object of)
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
 error: package or namespace load failed for 'RTN' in namespaceImportFrom(self, asNamespace(ns), from = from, except = except):
 'installTrChar' must be called on a CHARSXP, but got 'environment'
error: package or namespace load failed for 'Seurat' in `parent.env<-`(`*tmp*`, value = if (!is.null(data$enclos)) data$enclos else emptyenv()):
 Parameter is not an environment
> R_system_version()
Error in .make_numeric_version(x, strict, .standard_regexps()$valid_R_system_version,  : 

There are at least five different error reporting tips. I was going to go to GitHub or Stack Overflow for help. First, I looked at my computer environment:

> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.5.2

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

[1] zh_CN.UTF-8/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/zh_CN.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] compiler_4.1.1    minet_3.50.0      magrittr_2.0.1    limma_3.48.3      snow_0.4-4       
 [6] parallel_4.1.1    tools_4.1.1       igraph_1.2.7      RedeR_1.40.5      data.table_1.14.2
[11] pkgconfig_2.0.3  

I noticed two things. First, my Mac is not the latest version of the system. At present, it is macOS Big Sur 11.5.2, and the latest version is macOS Monterey. Other versions are as follows:


Latest version

macOS Monterey


macOS Big Sur


macOS Catalina


macOS Mojave


reference resources: https://support.apple.com/zh-cn/HT201260

Thinking about whether it was a new computer, but the operating system didn't keep up with the times, it took more than two hours to update the system. The embarrassing thing is that it still can't solve the depression of loading the same package and reporting errors every time.

At this time, the inspiration came. I went to the original R to load the same package, but there was no error. Let me fully understand that the so-called error reporting is actually a problem with the Rstudio tool! But I downloaded the latest version from the official website: https://www.rstudio.com/products/rstudio/download/

The latest version of Rstudio on the official website

At this time, I communicated with my friends and found that your rstudio is not a mark like the date displayed on the official website, but an ordinary version number, such as RStudio-1.4.1717.dmg

So I went to download the old version of rstudio. Sure enough, there were no strange errors in front this time.

But in fact, I can't understand the causes of the problems. I just use the thinking of control variable method to solve these errors.

Posted on Thu, 04 Nov 2021 05:28:48 -0400 by thaynejo