单细胞教程常见报错（原因 + 解决方法建议）完整合集---从此不怕分析“拦路虎”

#==========================================================================
#                       R语言错误整理集合
#==========================================================================
#2023年3月
#Error1：Error in .Call.graphics(C_palette2, .Call(C_palette2, NULL)) : invalid graphics state
@解决：dev.off()
#重新输入代码即可
# Error2: Failed to install 'unknown package' from GitHub:
#   Timeout was reached: [api.github.com] Connection timed out after 10001 milliseconds
#从devtools::install_github安装包的时候
@解决：稍安勿躁等待一下，多试几次，网络好了就可以，除非它的安装失效了（不要去弄乱七八糟的修改）
#github安装R包得时候
# Downloading GitHub repo zktuong/ktplots@HEAD
# Error: Failed to install 'ktplots' from GitHub:
#   lazy-load database '/home/R/x86_64-pc-linux-gnu-library/4.2/pkgbuild/R/pkgbuild.rdb' is corrupt
@解决：.rs.restartR()#重启Rstudio。但是之前环境保留
#ERROR：加载R包时候出现的  library(iTALK)
# Error: package or namespace load failed for 'iTALK':
#   Function found when exporting methods from the namespace 'DelayedArray' which is not S4 generic: 'aperm'
@解决:安装其他包：BiocManager::install('BiocGenerics',force = TRUE)
#Warning message:
#Removed 3 rows containing missing values (`geom_signif()`). 
#ggplot作图使用geom_signif添加显著性，出现这个警告，图上没有显著性标注
@解决:这是因为y轴范围的问题
@解决：加上：  scale_y_continuous()设置
#读取rds后缀的文件（直接双击打开）
#Error：Error in readRDS("~//Glia/Glia_inter.rds") : unknown input format
@解决:不用readRDS：使用load（就读取成功了）：
load("~/Glia/Glia_inter.rds")
#这是一个莫名其妙出现的error，其实也是一个warning，不管运行什么，会出现一个(converted from warning)
#例子
# 'select()' returned 1:1 mapping between keys and columns
# Error in bitr(markers_MG_clear$gene, fromType = "SYMBOL", toType = "ENTREZID",  : 
#                 (converted from warning) 6.53% of input gene IDs are fail to map...
# 这个错误总是阻碍运行程序
@解决:设置一下就ok了：options(warn=0)
#使用par layout图的时候出现错误
#Error in plot.new() : figure margins too large
@解决:par(mfrow = c(5,3), mar=c(1,1,1,1))#加上mar=c(1,1,1,1)就ok
#==========================================================================
#                       R语言错误整理集合
#==========================================================================
#2023年6月
#ERROR=========================================================================================
#场景：服务器安装velocyto.R 
#错误提示：
# /usr/bin/ld: cannot find -lboost_filesystem
# /usr/bin/ld: cannot find -lboost_system
# collect2: error: ld returned 1 exit status
# make: *** [/usr/share/R/share/make/shlib.mk:10: velocyto.R.so] Error 1
# ERROR: compilation failed for package ‘velocyto.R’
@解决办法：
##需要在终端安装两个包，然后返回重新安装就成功了，这也是这类错误的通用解决方式
# sudo apt-get install libboost-filesystem-dev
# sudo apt-get install libboost-system-dev
#ERROR=========================================================================================
#错误，install_github安装R包的时候，几次不成功，出现如下错误
# Error: Failed to install 'unknown package' from GitHub:
#   HTTP error 403.
# API rate limit exceeded for 106.58.229.196. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)
# 
#   Rate limit remaining: 0/60
#   Rate limit reset at: 2023-04-17 07:11:53 UTC
# 
#   To increase your GitHub API rate limit
#   - Use `usethis::create_github_token()` to create a Personal Access Token.
#   - Use `usethis::edit_r_environ()` and add the token as `GITHUB_PAT`.
#其实解决办法已经给出来了，要么等事件，要么解决
@解决办法：需要你有github账号，没有就注册一个
#运行：usethis::create_github_token()，登录github
#然后在页面底部点击Generate token
#在返回的页面中复制Personal access tokens (classic)，记得保存好
#在R里面运行：credentials::set_github_pat()， 在出现的框中粘贴你的Personal access tokens，点击ok
#然后继续安装install_github，就可以了
#ERROR=========================================================================================
#错误：scVelo运行RNA速率的时候
# AttributeError                            Traceback (most recent call last)
# Cell In[37], line 1
# ----> 1 scv.pl.velocity_embedding_stream(adata, basis='umap')
# 
# File ~/miniconda3/envs/jupyter/lib/python3.8/site-packages/scvelo/plotting/velocity_embedding_stream.py:252, in velocity_embedding_stream(adata, basis, vkey, density, smooth, min_mass, cutoff_perc, arrow_color, arrow_size, arrow_style, max_length, integration_direction, linewidth, n_neighbors, recompute, color, use_raw, layer, color_map, colorbar, palette, size, alpha, perc, X, V, X_grid, V_grid, sort_order, groups, components, legend_loc, legend_fontsize, legend_fontweight, xlabel, ylabel, title, fontsize, figsize, dpi, frameon, show, save, ax, ncols, **kwargs)
# 249 ax.streamplot(X_grid[0], X_grid[1], V_grid[0], V_grid[1], **stream_kwargs)
# 251 size = 8 * default_size(adata) if size is None else size
# --> 252 ax = scatter(
#   253     adata,
#   254     layer=layer,
#   255     color=color,
#   256     size=size,
#   257     title=title,
#   258     ax=ax,
#   259     zorder=0,
#   260     **scatter_kwargs,
#   261 )
# 262 if save is True:
#   263     save = "embedding_stream"
# 
# File ~/miniconda3/envs/jupyter/lib/python3.8/site-packages/scvelo/plotting/scatter.py:668, in scatter(adata, basis, x, y, vkey, color, use_raw, layer, color_map, colorbar, palette, size, alpha, linewidth, linecolor, perc, groups, sort_order, components, projection, legend_loc, legend_loc_lines, legend_fontsize, legend_fontweight, legend_fontoutline, legend_align_text, xlabel, ylabel, title, fontsize, figsize, xlim, ylim, add_density, add_assignments, add_linfit, add_polyfit, add_rug, add_text, add_text_pos, add_margin, add_outline, outline_width, outline_color, n_convolve, smooth, normalize_data, rescale_color, color_gradients, dpi, frameon, zorder, ncols, nrows, wspace, hspace, show, save, ax, **kwargs)
# 666     if not (add_outline is None or g_bool is None):
#   667         groups = add_outline
# --> 668     set_legend(
#   669         adata,
#   670         ax,
#   671         color,
#   672         legend_loc,
#   673         scatter_array,
#   674         legend_fontweight,
#   675         legend_fontsize,
#   676         legend_fontoutline,
#   677         legend_align_text,
#   678         groups,
#   679     )
# 680 if add_density:
#   681     plot_density(x, y, add_density, ax=ax)
# 
# File ~/miniconda3/envs/jupyter/lib/python3.8/site-packages/scvelo/plotting/utils.py:555, in set_legend(adata, ax, value_to_plot, legend_loc, scatter_array, legend_fontweight, legend_fontsize, legend_fontoutline, legend_align_text, groups)
# 553     legend_fontoutline = 1
# 554 obs_vals = adata.obs[value_to_plot]
# --> 555 obs_vals.cat.categories = obs_vals.cat.categories.astype(str)
# 556 color_keys = adata.uns[f"{value_to_plot}_colors"]
# 557 if isinstance(color_keys, dict):
#   
#   File ~/miniconda3/envs/jupyter/lib/python3.8/site-packages/pandas/core/base.py:178, in NoNewAttributesMixin.__setattr__(self, key, value)
# 172 if getattr(self, "__frozen", False) and not (
#   173     key == "_cache"
#   174     or key in type(self).__dict__
#   175     or getattr(self, key, None) is not None
#   176 ):
#   177     raise AttributeError(f"You cannot add any new attribute '{key}'")
# --> 178 object.__setattr__(self, key, value)
# 
# File ~/miniconda3/envs/jupyter/lib/python3.8/site-packages/pandas/core/accessor.py:99, in PandasDelegate._add_delegate_accessors.<locals>._create_delegator_property.<locals>._setter(self, new_values)
# 98 def _setter(self, new_values):
#   ---> 99     return self._delegate_property_set(name, new_values)
# 
# File ~/miniconda3/envs/jupyter/lib/python3.8/site-packages/pandas/core/arrays/categorical.py:2460, in CategoricalAccessor._delegate_property_set(self, name, new_values)
# 2459 def _delegate_property_set(self, name, new_values):
#   -> 2460     return setattr(self._parent, name, new_values)
# 
#!!!! AttributeError: can't set attribute
#原因：padans版本太高了，降低版本安装即可。之前的版本卸载
@解决办法：
pip uninstall pandas
pip install pandas==1.5.3 -i http://pypi.douban.com/simple/ --trusted-host pypi.douban.com
#ERROR=========================================================================================
#python：import scanpy报错
#可能是因为安装了别的包，在python import scanpy的时候报错
#TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict)
#原因是matplotlib的版本太高了，安装低于3.7的版本即可
pip install matplotlib==3.5 -i http://pypi.douban.com/simple/ --trusted-host pypi.douban.com
#然后继续import之后发现，又有新的错误
#ImportError: cannot import name 'is_categorical' from 'pandas.api.types' (C:\Users\AppData\Roaming\Python\Python39\site-packages\pandas\api\types\__init__.py)
#原因是pandas版本太高，我这里降低到1.4.2就可以用
pip install pandas==1.4.2 -i http://pypi.douban.com/simple/ --trusted-host pypi.douban.com
#ERROR=========================================================================================
#在使用library(cowplot)包组合多个list中的图片的时候出现这个错误
# Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto),  : 
#                      Viewport has zero dimension(s)
#不是代码和数据问题，原因是plot的窗口小了
@解决办法：把plot窗口拉大就可以了
#ERROR=========================================================================================
#numpy的报错
#AttributeError: module ‘numpy‘ has no attribute ‘float‘
#原因是numpy版本太高了，1.24.0才会出现
@解决办法：卸载目前的版本，安装之前的版本即可
pip uninstall numpy
pip install numpy==1.23.5
#ERROR=========================================================================================
#clusterProfiler做GSEA分析，莫名其妙出现如下的报错：
#Error in serialize(data, node$con) : error writing to connection
@解决办法：重启Rstudio，重现跑代码就ok了
#ERROR=========================================================================================
#clusterProfiler做分组GO分析，代码如下：
data_GO <- compareCluster(ENTREZID~group, data=data, fun="enrichGO", 
                          OrgDb="org.Mm.eg.db",ont = "BP",pAdjustMethod = "BH",
                          pvalueCutoff = 0.05,qvalueCutoff = 0.1)
data_GO_sim <- simplify(data_GO,cutoff=0.7, by="p.adjust", select_fun=min)
#在跑simplify的时候出现报错：
# Error in simplify(data_GO, cutoff = 0.7, by = "p.adjust", select_fun = min) : 
#   unused arguments (cutoff = 0.7, by = "p.adjust", select_fun = min)
@解决办法：#原因是函数串线了。指定R包即可
data_GO_sim <- clusterProfiler::simplify(data_GO,cutoff=0.7, by="p.adjust", select_fun=min)
#ERROR=========================================================================================
#monocle2 ordercell 或者 BEAM报错
@解决办法：不论是QQ群还是微信群我们发布过monocle2终极解决R包，安装这个包就不会出任何问题
#ERROR=========================================================================================
#加载R包的时候出错：Package ‘MatrixGenerics’ version 1.8.1 cannot be unloaded
#这个unloaded不一定是MatrixGenerics，也有可能遇上其他的。
@解决办法：你能信、折腾半天，解决办法居然是重启Rstusio，再次加载没毛病
#==========================================================================
#                       R语言错误整理集合
#==========================================================================
#2023年7月
#ERROR=========================================================================================
#运行monocle3，cds <- cluster_cells(cds)发生报错：
#Error in leidenbase::leiden_find_partition(graph_result[["g"]],  REAL() can only be applied to a 'numeric', not a 'NULL'
#原因：igraph的版本太高了，例如1.5.0
@解决办法：卸载原先的igraph，安装低版本的，我们测试1.3.5就可以了
remove.packages("igraph")
require(devtools)
install_version("igraph",version = '1.3.5', repos = "http://cran.us.r-project.org")
library(igraph)
library(monocle3)
#=========================================================================================
#运行monocle2出现错误
#Error in mutate()~:i In argument:pData(mouse monocle)$StateCaused by error:"CellDataSetuunable to find an inherited method for function pData' for signature
#原因：monoc3和monocle2冲突
@解决办法：一定记住，使用monocle2的时候不要加载monocle3，反之亦然
#=========================================================================================
#library(biomaRt)发生错误
# Error in { :
#     task 1 failed - "package or namespace load failed for 'dbplyr':
# .onLoad failed in loadNamespace() for 'dbplyr', details:
# call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
# error: error in contained classes ("character") for class "ident"; class definition removed from 'dbplyr'"
# 然后以为是没有加载dbplyr，继续 library(dbplyr), 发现还是出现这个错误
#这个error在很多地方出现，但是这里我成功解决的办法如下，对于其他的不知是否适用
@解决办法：
remove.packages("rlang")#删除这个包
install.packages("rlang")#重新安装，安装成功后重启Rstudio
library(rlang)
library(dbplyr)
library(biomaRt)#然后就成功了
#=========================================================================================
#R语言做某些图的时候出现纸样的Warning，导致图显示不全，或不正确
# Warning message:
#   Computation failed in `stat_stratum()`
# Caused by error in `default_missing()`:
#   ! could not find function "default_missing" 
#原因：dplyr或者ggalluvial包的版本低了
@解决办法：dplyr 1.1.2 ，ggalluvial 0.12.5即可
#=========================================================================================
#运行如下代码发生错误
celltype_ratio <-scedata@meta.data %>%
  group_by(group,celltype) %>%
  summarise(n=n()) %>%
  mutate(relative_freq = n/sum(n))
#Error
# Error in ~n()~:! Must only be used inside data-masking verbs like "mutate(), filter()', and "group by()'.Run rlang:;lasttrace()  to see where the error occurred.
@解决办法：summarise前面加上dplyr
celltype_ratio <-scedata@meta.data %>%
  group_by(group,celltype) %>%
  dplyr::summarise(n=n()) %>%
  mutate(relative_freq = n/sum(n))
#=========================================================================================
#Error
#这个也不能称之为一个错误
#事情是这样的，我不小心按了ctrl+shift+A键，导致Rstudio窗口全屏，退不出了
#网上查找发现，有人把四个窗口打乱了，可以使用快捷键恢复
@解决办法：Ctrl+Alt+Shift+0， 就会回复原来的布局了
#=========================================================================================
#Error
#pyscenic 分析第一步，终端中运行grn的时候报错
# preparing dask client
# parsing input
# creating dask graph
# 10 partitions
# computing dask graph
# not shutting down client, client was created externally
# finished
# distributed.worker - ERROR - Exception during execution of task infer_partial_network-1fad78969de74d650a57ebf5532dabbe.
#\\\
#反正很长的一串
#原因：大概率是因为线程数开大了，内存不够
@解决办法：减小num_workers数
#=========================================================================================
#Error
#Monocle2 plot_genes_branched_heatmap函数做分支热图的时候，出现如下错误
#Error in if (isSparseMatrix(exprs(X))) ! : the condition has length > 1
#按理来说，安装使用我们提过的monocle2终结解决版本，是不会有问题的，不过这个错误也是有一个解决办法
@解决办法：core=1的时候会报错，所以core设置为2或者其他
#==========================================================================
#                       R语言错误整理集合
#==========================================================================
#2023年8月
#ERROR=========================================================================================
#场景：Seurat做cellcycle，计算细胞周期的时候  SeuratObj[[x]] <- CellCycleScoring(SeuratObj[[x]], s.features = s.genes, g2m.features = g2m.genes, set.ident = FALSE)
#出现Error：
# Error in `cut_number()`:
#   ! Insufficient data values to produce 24 bins.
#原因：相同数值，0表达的太多，导致ggplot函数出错
@解决办法：第一种，先做跑NormalizeData，再计算周期就可以了，这种最好使
SeuratObj <- NormalizeData(SeuratObj, normalization.method = "LogNormalize")
@解决办法：第二种，在CreateSeuratObject的时候，min.cell设置为1
#ERROR=========================================================================================
此ERROR及解决办法分别由KS科研分享与服务VIP群“一位不愿意透露性别的学长”和“宁怡乐”贡献，感谢
#cellchat运行出现错误---这也是一个通用错误，其他运行中出现类似错误可考虑
# ce11chat <- projectData(ce11chat, PPI.human)
# Error in isTRUE(r <- .Ca11(Dim_validate, object,"Matrix"))object 'Dim_validate' not found
#原因：Matrix包版本的原因
@解决办法：Matrix1.6不兼容，要1.5-4.1才行，https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.5-4.1.tar.gz
#ERROR=========================================================================================
#单细胞Seurat分析FindNeighbors出错
# Computing nearest neighbor graph
# Computing SNN
# Error in validityMethod(as(object, superClass)) : 
#   object 'Csparse_validate' not found
#原因：Matrix包版本的问题
@解决办法：重新安装，换成1.5-3版本加载就可以了
#ERROR=========================================================================================
#单细胞数据分析PrepSCTIntegration出现错误
# Warning: SCT model not present in assay
# Error in scale.data[anchor.features, ] : 
#   no 'dimnames' attribute for array
#原因：流程不对，没有先跑SCTransform
@解决办法：先跑SCTransform，再跑PrepSCTIntegration
#ERROR=========================================================================================
#Complexheatmap做热图的时候出错，没有出现图
# Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto),  :    Viewport has zero dimension(s)
#原因：画板不够大
@解决办法：拉大画板即可。如果是需要直接保存为pdf，那么pdf导出尺寸设置大一点
#ERROR=========================================================================================
#使用Seurat或者其他S4对象的时候出现莫名奇妙的错误
# Error in `[[<-`(`*tmp*`, name, value = value) :    
#   [[<- defined for objects of type "S4" only for subclasses of environment
@解决办法：重启R环境就可以了
#ERROR=========================================================================================
library(biomaRt)#发生错误
# Error in { :
#     task 1 failed - "package or namespace load failed for 'dbplyr':
# .onLoad failed in loadNamespace() for 'dbplyr', details:
# call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
# error: error in contained classes ("character") for class "ident"; class definition removed from 'dbplyr'"
@解决办法：下载biomaRt最新版，http://www.bioconductor.org/packages/release/bioc/src/contrib/biomaRt_2.56.1.tar.gz
#本地安装，加载就可以了
library(biomaRt)
#ERROR=========================================================================================
# python出现如下错误
# AttributeError: module 'scipy.stats' has no attribute 'median_absolute_deviation'
#原因：scipy包1.9.0以上的版本，原来的'stats.median_absolute_deviation' 改成了“stats.median_abs_deviation‘
@解决办法：要么降低版本，要么修改这个名称
#ERROR=========================================================================================
#ARchR中plotMarkerHeatmap函数，或者Complexheatmap函数作图出现如下错误
# Error in magick_image_write_frame(image, format = format, i = i) : 
#   Image must have at least 1 frame to write a bitmap
#原因：热图行超过16000行就会出现这个错误
@解决办法：不要画这个大的数据
#==========================================================================
#                       R语言错误整理集合
#==========================================================================
#2023年9月
#ERROR=========================================================================================
#R语言运行出现如下的类似错误
Error in draw_axis(break_positions = guide$key[[aesthetic]], break_labels = guide$key$.label,  : 
                     lazy-load database 'C:/Users/tq199/AppData/Local/R/win-library/4.2/gtable/R/gtable.rdb' is corrupt
#一般都是：lazy-load database XXXXX is corrupt
@解决办法：重启Rstudio就可以了（一般这样可解决，如果不行，其他的问题需要进一步排除）
#ERROR=========================================================================================
#运行infercnv的时候出现以下报错
# Error: C stack usage 7969524 is too close to the limit
@解决办法：https://github.com/broadinstitute/infercnv/issues/335
#运行R之前在终端输入：ulimit -s unlimited
#ERROR=========================================================================================
#作图的时候出现如下的错误：
#Error in cairo::Cairo(type = "raster", width = width, height = height,图形API版本不相符
#或者..........Graphics API version mismatch
@解决办法：
#重新安装ragg包或者Cairo包
#其他的暂时不知
#R版本：4.2.1
#ERROR=========================================================================================
#ggtree作图或者其他相关的，作图有问题，或者有如下的warning：
#could not find function "offspring.tbl_tree_item"
@解决办法：重装ggtree
remotes::install_github('YuLab-SMU/ggtree')
#ERROR=========================================================================================
#服务器好端端的安装R包总是出现这样的错误
#error：ERROR: configuration failed for package ‘sodium’
@解决办法：终端中运行：
sudo apt install libsodium-dev
#然后在rsrudio种安装就没有问题了
#ERROR=========================================================================================
#做GSVA的时候出现如下的报错：或者其他的分析出现
# Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
#可能的原因是matrixStats包的问题
@解决办法：降低matrixStats版本或许能够解决
#ERROR=========================================================================================
#Signac做ATAC分析
# TSSPlot(combined, group.by = 'high.tss') + NoLegend()
# Error in TSSPlot(combined, group.by = "high.tss") : 
#   Position enrichment matrix not present in assay
#原因，在TSSEnrichment这里参数选择的问题
@解决办法： fast选择False
#ERROR=========================================================================================
#Signac做ATAC分析
combined <- RunSVD(combined)
# Running SVD
# Error in irlba(A = t(x = object), nv = n, work = irlba.work, tol = tol) : 
#   function 'as_cholmod_sparse' not provided by package 'Matrix'
@解决办法：可能有用的方法： 卸载之前的irlba，重新本地安装irlba，重启R
#ERROR=========================================================================================
#保存文件的时候出现如下报错：
# Error in save(Coembedding, file = "Coembedding.RData") : 
#   error writing to connection
#原因：磁盘没有空间了
@解决办法：清理空间

#==========================================================================

#                       R语言错误整理集合

#==========================================================================
#2024年

#ERROR=========================================================================================
#当你跑一些代码的时候，可能是GSVA、可能是Seurat、SCT或者其他，出现如下错误：
# Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.

#原因：matrixStats 包版本的问题
@解决办法：使用1.1.0的matrixStats
remotes::install_version("matrixStats", version="1.1.0")


#ERROR=========================================================================================
#python运行网络图相关，出现如下error
# AttributeError: 'NoneType' object has no attribute 'render'
@解决办法：
pip install pyvis==0.3.1 -i http://pypi.douban.com/simple/ --trusted-host pypi.douban.com


#ERROR=========================================================================================
#当你运行peaks annotation的时候，出现如下的错误：
DAR.Anno <- annotatePeak(all_dar.gr, tssRegion=c(-3000, 3000), TxDb = txdb, annoDb="org.Hs.eg.db")
# Error in (function (classes, fdef, mtable)  : 
#             unable to find an inherited method for function ‘NSBS’ for signature ‘"SortedByQueryHits"’

@解决办法：需要再染色体前面添加chr

GenomeInfoDb::seqlevels(all_dar.gr)
all_dar.gr <- diffloop::addchr(all_dar.gr)
DAR.Anno <- annotatePeak(all_dar.gr, tssRegion=c(-3000, 3000), TxDb = txdb, annoDb="org.Hs.eg.db")


#ERROR=========================================================================================
#安装、加载、或者使用的时候出现类似的错误，.rdb' is corrupt
# Error in get(Info[i, 1], envir = env) : 
#   lazy-load database '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/lme4/R/lme4.rdb' is corrupt

@解决办法：重启R可能会解决你的问题
.rs.restartR()


#ERROR=========================================================================================
#安装monocle3或者其他包的时候出现这样的错误：
# configure: error: gdal-config not found or not executable.
# ERROR: configuration failed for package ‘sf’

@解决办法：终端安装GDAL可能会解决你的问题
sudo apt-get install libgdal-dev


#ERROR=========================================================================================
#scATAC数据分析：：：：cicero  分析出现如下错误
#Error: methods::is(object = cds, class2 = "cell_data_set") is not TRUE
#原因是monocle3依赖的问题
@解决办法：卸载之前的cicero，按照如下的方式安装，就可以了
devtools::install_github("cole-trapnell-lab/cicero-release", ref = "monocle3")


#ERROR=========================================================================================
#跑 cellchat  selectK 的时候出现的错误
#运行这一句：
object.list[[1]] <- netAnalysis_computeCentrality(object.list[[1]], slot.name = "netP")
selectK(object.list[[1]], pattern = "outgoing")

# Timing stopped at: 0.014 0.003 0.017
# Timing stopped at: 0.005 0 0.005
# Timing stopped at: 0.003 0 0.004
# Timing stopped at: 0.013 0 0.013
# Timing stopped at: 0.003 0 0.003
# Timing stopped at: 0.002 0.008 0.011
# Timing stopped at: 0.003 0 0.004
# Timing stopped at: 0.004 0 0.007
# Timing stopped at: 0.005 0 0.007
# Error in (function (...)  : All the runs produced an error:
#             -#1 [r=2] -> none of the packages are loaded [in call to 'path.package']
#             -#2 [r=3] -> none of the packages are loaded [in call to 'path.package']
#             -#3 [r=4] -> none of the packages are loaded [in call to 'path.package']
#             -#4 [r=5] -> none of the packages are loaded [in call to 'path.package']
#             -#5 [r=6] -> none of the packages are loaded [in call to 'path.package']
#             -#6 [r=7] -> none of the packages are loaded [in call to 'path.package']
#             -#7 [r=8] -> none of the packages are loaded [in call to 'path.package']
#             -#8 [r=9] -> none of the packages are loaded [in call to 'path.package']
#             -#9 [r=10] -> none of the packages are loaded [in call to 'path.package']


#原因：有些包没有加载
@解决办法：感谢KS科研分享与服务1群的 L。加载相关的包就可以了
library(NMF)
library(ggalluvial)

#ERROR=========================================================================================
#安装了最新版的DoubletFinder
remotes::install_github('chris-mcginnis-ucsf/DoubletFinder')
library(DoubletFinder)

#但是在运行的时候第一步就出现了错误
#Error in seu@assays$RNA$counts : $ operator not defined for this S4 class

#原因：seurat obj是Seurat V4和 SeuratObject V4构建的
#安装别人fix的版本就好了
@解决办法：remotes::install_github('lzmcboy/DoubletFinder_204_fix')


#后面测试之后我大概找到了原因
#如果你用seurat V5是不会有任何问题的
#如果你用了Seurat V4但是SeuratObject 是V5构建的数据，也不会出错



#ERROR=========================================================================================
#pyscenic分析  grn 报错：
#TypeError: Must supply at least one delayed object
#解决办法：
pip install distributed==2023.12.1

#参考：https://github.com/aertslab/pySCENIC/issues/525


#ERROR=========================================================================================
#Cellchat 作图的时候出现错误
Error in Ops.data.frame(guide_loc, panel_loc) : 
  ‘==’ only defined for equally-sized data frames

#seurat Dimplot出现报错
Error in Ops.data.frame(guide_loc, panel_loc) : 
  ‘==’ only defined for equally-sized data frames

#可能原因；ggplot2版本问题，太高？
#解决办法: ggplot2版本使用3.4.0

@解决办法
remotes::install_version("ggplot2", version = "3.4.4", repos = "http://cran.us.r-project.org")


#ERROR=========================================================================================
#R语言作图的时候出现如下报错
Error in .Call.graphics(C_palette2, .Call(C_palette2, NULL)) : 
  invalid graphics state

#可能原因；图太多太大超过rstudio的承受能力
@解决办法
#清空环境中的作图，重新画就可以了



#ERROR=========================================================================================
#单细胞seurat obj使用subset函数提取亚群出现如下错误
# Error in isVirtualExt(exti) :
#   trying to get slot "virtual" from an object of a basic class ("NULL") with no slots

#可能原因：seurat是4.0， SeuratObject 5.0
@解决办法
#两者需要一致，要么都是4，要么都是5


#ERROR=========================================================================================
#Nebulosa包做单细胞密度图或者irGSEA包 plot的时候出现如下报错
# Error in as.vector(x, "character") : 
#   cannot coerce type 'environment' to vector of type 'character'
#可能原因：不知
@解决办法
#卸载掉原来的Nebulosa包，重装
devtools::install_github("powellgenomicslab/Nebulosa") 


#ERROR=========================================================================================
#pyscenic grn 第一步发生报错：
# TypeError: Must supply at least one delayed object
@解决办法
https://github.com/aertslab/pySCENIC/issues/561


#ERROR=========================================================================================
#使用devtools::install_github安装某些包的时候，总是不成功，无法下载，很多时候github都不知道在哪下载安装包
devtools::install_github('shenorrlab/bseqsc')
Downloading GitHub repo shenorrlab/bseqsc@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
cannot open URL 'https://api.github.com/repos/shenorrlab/bseqsc/tarball/HEAD'


@解决办法
#其实很简单，哪个error后面都提供链接了，R下载不成，就把链接复制到浏览器，然后就可以下载包本地安装了                         



#ERROR=========================================================================================
#使用patchwork 拼图出现如下报错
# Error in theme[[element]]
# attempt to select more than one element in vectorIndex

#可能原因：包版本的问题，1.3会出现问题
@解决办法
#降低包的版本，1.2就可以了



#ERROR=========================================================================================
#ubbantu linux终端运行python代码出现如下报错：代码没有错误的情况下
#SyntaxError: invalid non-printable character U+00A0

#可能原因：代码是从windows复制粘贴到ubuntu上，复制的代码中空格和Python中的格式不一样造成的
@解决办法
#手动输入代码


#ERROR=========================================================================================
#运行代码出现如下errror
#Error in `validObject()`: ! 类别为"Graph"的对象不对: superclass "mMatrix" not defined in the environment of the object's class

#可能原因：还是Matrix的毛病
@解决办法：
remotes::install_version("Matrix", "1.6.1")


#ERROR=========================================================================================
#seurat 分析 RunUMAP的时候报错：
# Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters) : 
#   function 'sexp_as_cholmod_sparse' not provided by package 'Matrix'
#可能原因：irlba包在作妖

@解决办法：卸载之前的，重启R安装irlba就解决了
install.packages("irlba", type="source")



#ERROR=========================================================================================
#运行某些代码出现如下得报错：
# Error in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) :
#   invalid non-character version specification 'x' (type: double) 

#可能原因：ggplot2版本得问题

@解决办法：安装最新版？？？ ggplot2 3.5.1

#ERROR=========================================================================================
#可能你在R中导入h5ad数据的时候出现如下报错：
#Error in h5ad loading: invalid class “dgRMatrix” object: 'Dim' slot does not have length 2

@解决办法：我倾向于第二种

#1、在环境中将scipy版本降低为1.11以下
#2、卸载原先的reticulate包，重新安装最新的：remotes::install_github("rstudio/reticulate")


#ERROR=========================================================================================
#Windows R包安装出现报错
# Error: Failed to install 'x' from GitHub:
#   Git does not seem to be installed on your system.


@解决办法：安装Git
#这里下载Git安装包，按默认安装好就可以了， https://git-scm.com/downloads/win


#ERROR=========================================================================================
#monocle3  graph_test 出现错误
# >mycds1_res <- graph_test(mycds1, neighbor_graph="principal_graph", cores=4)
# 错误: make_nn_matrix: the subject_matrix object must be of type matrix

@解决办法：参考---https://github.com/cole-trapnell-lab/monocle3/issues/617


#ERROR=========================================================================================
#signac 分析scATAC数据使用 ClosetFeature函数的时候出现如下报错：
# Error in .Call2("C_find_overlaps_in_groups_NCList", start(q), end(q),  : 
#                   build_NCList: memory allocation failed

#原因：设备问题，不是其他的就是内存不够了，因为用的笔记本

@解决办法：使用服务器或者运行内存大的设备就不会有这个问题


#ERROR=========================================================================================
# circlize包函数circos.heatmap，或者其他函数作图出现这个错误
# Error in split.default(seq_len(nrow(mat)), split) : 
#   group length is 0 but data length > 0

#原因：大概率再plot的时候没有清空当前plot

@解决办法：circos.clear()，然后再plot



#ERROR=========================================================================================
#scFEA 发生如下报错
#TypeError: can't convert np.ndarray of type numpy.object_. The only supported types are: float64, float32, float16, complex64, complex128, int64, int32, int16, int8, uint8, and bool.
#可能原因：90%是因为弄错了文件，human用小鼠的，或者小鼠的用human的

@解决办法：检查文件



#ERROR=========================================================================================
#scanpy分析，比如我修改了细胞注释，直接覆盖了原始列，画图的时候sc.pl.umap(adata,color='cell_type')，出现了这样的报错
#ValueError: zip() argument 2 is longer than argument 1


#原因：
#Scanpy 在绘图时自动为类别生成颜色，但颜色数和分类数不一致
#adata.obs['cell_type'] 中的分类值（比如 'A', 'B', 'E'）有 3 个；
#但 .uns['cell_type_colors'] 中可能还保留着旧的 4 个颜色值（A, B, C, D）

@解决办法：
#1-清除或更新颜色信息：

if 'cell_type_colors' in adata.uns:
  del adata.uns['cell_type_colors']

#2-手动设置新的颜色映射
#有几种类别就设置几种颜色
adata.uns['cell_type_colors'] = ['#1f77b4', '#ff7f0e', '#2ca02c'] 
sc.pl.umap(adata, color='cell_type')



#有用小代码
brain_Sag.merge@meta.data$sample <-  unlist(lapply(strsplit(row.names(brain_Sag.merge@meta.data), split = "_"), function(x) x[[2]]))

#mac 问题解决
https://zhuanlan.zhihu.com/p/111748325


#ERROR=========================================================================================
#nichenetr运行如下代码出现报错：

ligand_activities = ligand_activities %>% arrange(-pearson) %>% mutate(rank = rank(desc(pearson)))

# Error: Problem with `mutate()` column `rank`.
# ? `rank = rank(desc(pearson))`.
# x error in evaluating the argument 'x' in selecting a method for function 'rank': unable to find an inherited method for function desc

#原因：包冲突，这里的desc函数是dplyr包的
@解决办法：
ligand_activities = ligand_activities %>% arrange(-pearson) %>% mutate(rank = base::rank(dplyr::desc(pearson)))



#ERROR=========================================================================================
#ggplot2作图报错，不论是ggplot2 plot还是其他包依赖ggplot2作图报错
ggplot(pb_mds, aes(MDS1, MDS2, col = cluster_id, shape = group_id)) + 
  geom_point(size = 3, alpha = 0.8)
#：Error in ggplot(pb_mds, aes(MDS1, MDS2, col = cluster_id, shape = group_id)) + : non-numeric argument to binary operator

#原因：包不兼容的问题，这个报错出现在ggplot2 4.0.0版本


@解决办法：降低版本，安装3.5.2
devtools::install_version("ggplot2", version = "3.5.2", repos = "https://cran.r-project.org")

#ERROR=========================================================================================
#单细胞转录组SCTransform分析或者其他例如singleR报错：
#Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.

#原因包的问题：matrixStats
@解决办法：一说降低matrixStats版本至1.1.0及以下，但是会引起包的冲突
#根本解决办法：BiocManager::install(version = "3.20")，重装升级，视自己R版本决定，我是R4.0